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Bork GroupPublications

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene expression profiling.
van Noort, V.V., Scholch, S., Iskar, M., Zeller, G., Ostertag, K., Schweitzer, C., Werner, K., Weitz, J., Koch, M. & Bork, P.
Cancer Res. 2014 Jul 18. pii: canres.3540.2013. Europe PMC

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen, H.B., Almeida, M., Juncker, A.S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D.R., Gautier, L., Pedersen, A.G., Le Chatelier, E., Pelletier, E., Bonde, I., Nielsen, T., Manichanh, C., Arumugam, M., Batto, J.M., Quintanilha Dos Santos, M.B., Blom, N., Borruel, N., Burgdorf, K.S., Boumezbeur, F., Casellas, F., Dore, J., Dworzynski, P., Guarner, F., Hansen, T., Hildebrand, F., Kaas, R.S., Kennedy, S., Kristiansen, K., Kultima, J.R., Leonard, P., Levenez, F., Lund, O., Moumen, B., Le Paslier, D., Pons, N., Pedersen, O., Prifti, E., Qin, J., Raes, J., Sorensen, S., Tap, J., Tims, S., Ussery, D.W., Yamada, T., Renault, P., Sicheritz-Ponten, T., Bork, P., Wang, J., Brunak, S. & Ehrlich, S.D.
Nat Biotechnol. 2014 Jul 6. doi: 10.1038/nbt.2939. Europe PMC

An integrated catalog of reference genes in the human gut microbiome.
Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J.R., Prifti, E., Nielsen, T., Juncker, A.S., Manichanh, C., Chen, B., Zhang, W., Levenez, F., Wang, J., Xu, X., Xiao, L., Liang, S., Zhang, D., Zhang, Z., Chen, W., Zhao, H., Al-Aama, J.Y., Edris, S., Yang, H., Wang, J., Hansen, T., Nielsen, H.B., Brunak, S., Kristiansen, K., Guarner, F., Pedersen, O., Dore, J., Ehrlich, S.D., Bork, P. & Wang, J.
Nat Biotechnol. 2014 Jul 6. doi: 10.1038/nbt.2942. Europe PMC

A fair comparison.
Costea, P.I., Zeller, G., Sunagawa, S. & Bork, P.
Nat Methods. 2014 Apr;11(4):359. doi: 10.1038/nmeth.2897. Europe PMC

Classification and quantification of bacteriophage taxa in human gut metagenomes.
Waller, A.S., Yamada, T., Kristensen, D.M., Kultima, J.R., Sunagawa, S., Koonin, E.V. & Bork, P.
ISME J. 2014 Mar 13. doi: 10.1038/ismej.2014.30. Europe PMC

Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs.
Gallina, A.M., Bork, P. & Bordo, D.
J Mol Recognit. 2014 Feb;27(2):65-72. doi: 10.1002/jmr.2332. Europe PMC

Metagenomic insights into the human gut resistome and the forces that shape it.
Forslund, K., Sunagawa, S., Coelho, L.P. & Bork, P.
Bioessays. 2014 Jan 29. doi: 10.1002/bies.201300143. Europe PMC

A quantitative liposome microarray to systematically characterize protein-lipid interactions.
Saliba, A.E., Vonkova, I., Ceschia, S., Findlay, G.M., Maeda, K., Tischer, C., Deghou, S., van Noort, V., Bork, P., Pawson, T., Ellenberg, J. & Gavin, A.C.
Nat Methods. 2014 Jan;11(1):47-50. doi: 10.1038/nmeth.2734. Epub 2013 Nov 24. Europe PMC

eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldon, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L.J., von Mering, C. & Bork, P.
Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9. doi: 10.1093/nar/gkt1253.Epub 2013 Dec 1. Europe PMC

STITCH 4: integration of protein-chemical interactions with user data.
Kuhn, M., Szklarczyk, D., Pletscher-Frankild, S., Blicher, T.H., von Mering, C., Jensen, L.J. & Bork, P.
Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207.Epub 2013 Nov 28. Europe PMC

Evolution and functional cross-talk of protein post-translational modifications.
Beltrao, P., Bork, P., Krogan, N.J. & van Noort, V.
Mol Syst Biol. 2013 Dec 22;9:714. doi: 10.1002/msb.201304521. Print 2013. Europe PMC

Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., de Vos, W.M., Wang, J., Li, J., Dore, J., Ehrlich, S.D., Stamatakis, A. & Bork, P.
Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20. Europe PMC

Accurate and universal delineation of prokaryotic species.
Mende, D.R., Sunagawa, S., Zeller, G. & Bork, P.
Nat Methods. 2013 Sep;10(9):881-4. doi: 10.1038/nmeth.2575. Epub 2013 Jul 28. Europe PMC

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
Hingamp, P., Grimsley, N., Acinas, S.G., Clerissi, C., Subirana, L., Poulain, J., Ferrera, I., Sarmento, H., Villar, E., Lima-Mendez, G., Faust, K., Sunagawa, S., Claverie, J.M., Moreau, H., Desdevises, Y., Bork, P., Raes, J., de Vargas, C., Karsenti, E., Kandels-Lewis, S., Jaillon, O., Not, F., Pesant, S., Wincker, P. & Ogata, H.
ISME J. 2013 Sep;7(9):1678-95. doi: 10.1038/ismej.2013.59. Epub 2013 Apr 11. Europe PMC

Richness of human gut microbiome correlates with metabolic markers.
Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.M., Kennedy, S., Leonard, P., Li, J., Burgdorf, K., Grarup, N., Jorgensen, T., Brandslund, I., Nielsen, H.B., Juncker, A.S., Bertalan, M., Levenez, F., Pons, N., Rasmussen, S., Sunagawa, S., Tap, J., Tims, S., Zoetendal, E.G., Brunak, S., Clement, K., Dore, J., Kleerebezem, M., Kristiansen, K., Renault, P., Sicheritz-Ponten, T., de Vos, W.M., Zucker, J.D., Raes, J., Hansen, T., Bork, P., Wang, J., Ehrlich, S.D., Pedersen, O., Guedon, E., Delorme, C., Layec, S., Khaci, G., van de Guchte, M., Vandemeulebrouck, G., Jamet, A., Dervyn, R., Sanchez, N., Maguin, E., Haimet, F., Winogradski, Y., Cultrone, A., Leclerc, M., Juste, C., Blottiere, H., Pelletier, E., LePaslier, D., Artiguenave, F., Bruls, T., Weissenbach, J., Turner, K., Parkhill, J., Antolin, M., Manichanh, C., Casellas, F., Boruel, N., Varela, E., Torrejon, A., Guarner, F., Denariaz, G., Derrien, M., van Hylckama Vlieg, J.E., Veiga, P., Oozeer, R., Knol, J., Rescigno, M., Brechot, C., M'Rini, C., Merieux, A. & Yamada, T.
Nature. 2013 Aug 29;500(7464):541-6. doi: 10.1038/nature12506. Europe PMC

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
Logares, R., Sunagawa, S., Salazar, G., Cornejo-Castillo, F.M., Ferrera, I., Sarmento, H., Hingamp, P., Ogata, H., de Vargas, C., Lima-Mendez, G., Raes, J., Poulain, J., Jaillon, O., Wincker, P., Kandels-Lewis, S., Karsenti, E., Bork, P. & Acinas, S.G.
Environ Microbiol. 2013 Aug 18. doi: 10.1111/1462-2920.12250. Europe PMC

Country-specific antibiotic use practices impact the human gut resistome.
Forslund, K., Sunagawa, S., Kultima, J.R., Mende, D.R., Arumugam, M., Typas, A. & Bork, P.
Genome Res. 2013 Jul;23(7):1163-9. doi: 10.1101/gr.155465.113. Epub 2013 Apr 8. Europe PMC

Human monogenic disease genes have frequently functionally redundant paralogs.
Chen, W.H., Zhao, X.M., van Noort, V. & Bork, P.
PLoS Comput Biol. 2013;9(5):e1003073. doi: 10.1371/journal.pcbi.1003073. Epub2013 May 16. Europe PMC

Systematic identification of proteins that elicit drug side effects.
Kuhn, M., Al Banchaabouchi, M., Campillos, M., Jensen, L.J., Gross, C., Gavin, A.C. & Bork, P.
Mol Syst Biol. 2013;9:663. doi: 10.1038/msb.2013.10. Europe PMC

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.
Iskar, M., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K.H., Runz, H., Gavin, A.C., Pepperkok, R., van Noort, V. & Bork, P.
Mol Syst Biol. 2013;9:662. doi: 10.1038/msb.2013.20. Europe PMC

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.
Ori, A., Banterle, N., Iskar, M., Andres-Pons, A., Escher, C., Khanh Bui, H., Sparks, L., Solis-Mezarino, V., Rinner, O., Bork, P., Lemke, E.A. & Beck, M.
Mol Syst Biol. 2013 Mar 19;9:648. doi: 10.1038/msb.2013.4. Europe PMC

Genomic variation landscape of the human gut microbiome.
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., Kota, K., Sunyaev, S.R., Weinstock, G.M. & Bork, P.
Nature. 2013 Jan 3;493(7430):45-50. doi: 10.1038/nature11711. Epub 2012 Dec 5. Europe PMC

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini, C., Iorio, F., Goncalves, E., Iskar, M., Klabunde, T., Bork, P. & Saez-Rodriguez, J.
Bioinformatics. 2013 Jan 1;29(1):132-4. doi: 10.1093/bioinformatics/bts656. Epub2012 Nov 4. Europe PMC

Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.
Kristensen, D.M., Waller, A.S., Yamada, T., Bork, P., Mushegian, A.R. & Koonin, E.V.
J Bacteriol. 2013 Mar;195(5):941-50. doi: 10.1128/JB.01801-12. Epub 2012 Dec 7. Europe PMC

The microbiome explored: recent insights and future challenges.
Blaser, M., Bork, P., Fraser, C., Knight, R. & Wang, J.
Nat Rev Microbiol. 2013 Mar;11(3):213-7. doi: 10.1038/nrmicro2973. Epub 2013 Feb4. Europe PMC

Experimental characterization of the human non-sequence-specific nucleic acid interactome.
Durnberger, G., Burckstummer, T., Huber, K., Giambruno, R., Doerks, T., Karayel, E., Burkard, T.R., Kaupe, I., Muller, A.C., Schonegger, A., Ecker, G.F., Lohninger, H., Bork, P., Bennett, K.L., Superti-Furga, G. & Colinge, J.
Genome Biol. 2013 Jul 31;14(7):R81. Europe PMC

Consistent mutational paths predict eukaryotic thermostability.
van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C., Falk, S., Mende, D.R., Sinning, I., Hurt, E. & Bork, P.
BMC Evol Biol. 2013 Jan 10;13:7. doi: 10.1186/1471-2148-13-7. Europe PMC

Role for urea in nitrification by polar marine Archaea.
Alonso-Saez, L., Waller, A.S., Mende, D.R., Bakker, K., Farnelid, H., Yager, P.L., Lovejoy, C., Tremblay, J.E., Potvin, M., Heinrich, F., Estrada, M., Riemann, L., Bork, P., Pedros-Alio, C. & Bertilsson, S.
Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17989-94. doi:10.1073/pnas.1201914109. Epub 2012 Oct 1. Europe PMC

MOCAT: a metagenomics assembly and gene prediction toolkit.
Kultima, J.R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D.R., Arumugam, M., Pan, Q., Liu, B., Qin, J., Wang, J. & Bork, P.
PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17. Europe PMC

Drug discovery in the age of systems biology: the rise of computational approaches for data integration.
Iskar, M., Zeller, G., Zhao, X.M., van Noort, V. & Bork, P.
Curr Opin Biotechnol. 2012 Aug;23(4):609-16. doi: 10.1016/j.copbio.2011.11.010.Epub 2011 Dec 5. Europe PMC

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.
Zoetendal, E.G., Raes, J., van den Bogert, B., Arumugam, M., Booijink, C.C., Troost, F.J., Bork, P., Wels, M., de Vos, W.M. & Kleerebezem, M.
ISME J. 2012 Jul;6(7):1415-26. doi: 10.1038/ismej.2011.212. Epub 2012 Jan 19. Europe PMC

Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age.
Chen, W.H., Trachana, K., Lercher, M.J. & Bork, P.
Mol Biol Evol. 2012 Jul;29(7):1703-6. doi: 10.1093/molbev/mss014. Epub 2012 Jan19. Europe PMC

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins.
Doerks, T., van Noort, V., Minguez, P. & Bork, P.
PLoS One. 2012;7(4):e34302. doi: 10.1371/journal.pone.0034302. Epub 2012 Apr 2. Europe PMC

A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL.
Haemmerling, S., Behnisch, W., Doerks, T., Korbel, J.O., Bork, P., Moog, U., Hentze, S., Grasshoff, U., Bonin, M., Riess, O., Janssen, J.W., Jauch, A., Bartram, C.R., Reinhardt, D., Koch, K.A., Bandapalli, O.R. & Kulozik, A.E.
Br J Haematol. 2012 Apr;157(2):180-7. doi: 10.1111/j.1365-2141.2012.09028.x. Epub2012 Feb 1. Europe PMC

Assessment of metagenomic assembly using simulated next generation sequencing data.
Mende, D.R., Waller, A.S., Sunagawa, S., Jarvelin, A.I., Chan, M.M., Arumugam, M., Raes, J. & Bork, P.
PLoS One. 2012;7(2):e31386. Epub 2012 Feb 23. Europe PMC

The Tenth Asia Pacific Bioinformatics Conference (APBC 2012). Introduction.
Chen, Y.P. & Bork, P.
BMC Genomics. 2012;13 Suppl 1:I1. doi: 10.1186/1471-2164-13-S1-I1. Epub 2012 Jan17. Europe PMC

SMART 7: recent updates to the protein domain annotation resource.
Letunic, I., Doerks, T. & Bork, P.
Nucleic Acids Res. 2012 Jan;40(Database issue):D302-5. doi: 10.1093/nar/gkr931.Epub 2011 Nov 3. Europe PMC

STITCH 3: zooming in on protein-chemical interactions.
Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, L.J. & Bork, P.
Nucleic Acids Res. 2012 Jan;40(Database issue):D876-80. doi: 10.1093/nar/gkr1011.Epub 2011 Nov 9. Europe PMC

OGEE: an online gene essentiality database.
Chen, W.H., Minguez, P., Lercher, M.J. & Bork, P.
Nucleic Acids Res. 2012 Jan;40(Database issue):D901-6. doi: 10.1093/nar/gkr986.Epub 2011 Nov 10. Europe PMC

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L.J., von Mering, C. & Bork, P.
Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. Epub 2011 Nov 16. Europe PMC

InterPro in 2011: new developments in the family and domain prediction database.
Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S., de Castro, E., Coggill, P., Corbett, M., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Fraser, M., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., McMenamin, C., Mi, H., Mutowo-Muellenet, P., Mulder, N., Natale, D., Orengo, C., Pesseat, S., Punta, M., Quinn, A.F., Rivoire, C., Sangrador-Vegas, A., Selengut, J.D., Sigrist, C.J., Scheremetjew, M., Tate, J., Thimmajanarthanan, M., Thomas, P.D., Wu, C.H., Yeats, C. & Yong, S.Y.
Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. Epub 2011 Nov 16. Europe PMC

Transcription start site associated RNAs in bacteria.
Yus, E., Guell, M., Vivancos, A.P., Chen, W.H., Lluch-Senar, M., Delgado, J., Gavin, A.C., Bork, P. & Serrano, L.
Mol Syst Biol. 2012 May 22;8:585. doi: 10.1038/msb.2012.16. Europe PMC

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.
Yamada, T., Waller, A.S., Raes, J., Zelezniak, A., Perchat, N., Perret, A., Salanoubat, M., Patil, K.R., Weissenbach, J. & Bork, P.
Mol Syst Biol. 2012 May 8;8:581. doi: 10.1038/msb.2012.13. Europe PMC

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.
van Noort, V., Seebacher, J., Bader, S., Mohammed, S., Vonkova, I., Betts, M.J., Kuhner, S., Kumar, R., Maier, T., O'Flaherty, M., Rybin, V., Schmeisky, A., Yus, E., Stulke, J., Serrano, L., Russell, R.B., Heck, A.J., Bork, P. & Gavin, A.C.
Mol Syst Biol. 2012 Feb 28;8:571. doi: 10.1038/msb.2012.4. Europe PMC

Deciphering a global network of functionally associated post-translational modifications.
Minguez, P., Parca, L., Diella, F., Mende, D.R., Kumar, R., Helmer-Citterich, M., Gavin, A.C., van Noort, V. & Bork, P.
Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31. Europe PMC

Prediction of drug combinations by integrating molecular and pharmacological data.
Zhao, X.M., Iskar, M., Zeller, G., Kuhn, M., Noort, V. & Bork, P.
PLoS Comput Biol. 2011 Dec;7(12):e1002323. Epub 2011 Dec 29. Europe PMC

A holistic approach to marine eco-systems biology.
Karsenti, E., Acinas, S.G., Bork, P., Bowler, C., De Vargas, C., Raes, J., Sullivan, M., Arendt, D., Benzoni, F., Claverie, J.M., Follows, M., Gorsky, G., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Krzic, U., Not, F., Ogata, H., Pesant, S., Reynaud, E.G., Sardet, C., Sieracki, M.E., Speich, S., Velayoudon, D., Weissenbach, J. & Wincker, P.
PLoS Biol. 2011 Oct;9(10):e1001177. doi: 10.1371/journal.pbio.1001177. Epub 2011Oct 18. Europe PMC

Orthology prediction methods: a quality assessment using curated protein families.
Trachana, K., Larsson, T.A., Powell, S., Chen, W.H., Doerks, T., Muller, J. & Bork, P.
Bioessays. 2011 Oct;33(10):769-80. doi: 10.1002/bies.201100062. Epub 2011Aug 19. Europe PMC

Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile.
Amlacher, S., Sarges, P., Flemming, D., van Noort, V., Kunze, R., Devos, D.P., Arumugam, M., Bork, P. & Hurt, E.
Cell. 2011 Jul 22;146(2):277-89. doi: 10.1016/j.cell.2011.06.039. Europe PMC

iPath2.0: interactive pathway explorer.
Yamada, T., Letunic, I., Okuda, S., Kanehisa, M. & Bork, P.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W412-5. Epub 2011 May 5. Europe PMC

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.
Letunic, I. & Bork, P.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W475-8. Epub 2011 Apr 5. Europe PMC

Enterotypes of the human gut microbiome.
Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Antolin, M., Artiguenave, F., Blottiere, H.M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Foerstner, K.U., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Huber, W., van Hylckama-Vlieg, J., Jamet, A., Juste, C., Kaci, G., Knol, J., Lakhdari, O., Layec, S., Le Roux, K., Maguin, E., Merieux, A., Melo Minardi, R., M'rini, C., Muller, J., Oozeer, R., Parkhill, J., Renault, P., Rescigno, M., Sanchez, N., Sunagawa, S., Torrejon, A., Turner, K., Vandemeulebrouck, G., Varela, E., Winogradsky, Y., Zeller, G., Weissenbach, J., Ehrlich, S.D. & Bork, P.
Nature. 2011 May 12;473(7346):174-80. Epub 2011 Apr 20. Europe PMC

The ecoresponsive genome of Daphnia pulex.
Colbourne, J.K., Pfrender, M.E., Gilbert, D., Thomas, W.K., Tucker, A., Oakley, T.H., Tokishita, S., Aerts, A., Arnold, G.J., Basu, M.K., Bauer, D.J., Caceres, C.E., Carmel, L., Casola, C., Choi, J.H., Detter, J.C., Dong, Q., Dusheyko, S., Eads, B.D., Frohlich, T., Geiler-Samerotte, K.A., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E.V., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J.R., Muller, J., Pangilinan, J., Patwardhan, R.P., Pitluck, S., Pritham, E.J., Rechtsteiner, A., Rho, M., Rogozin, I.B., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y.I., Yamagata, H., Yamada, T., Ye, Y., Shaw, J.R., Andrews, J., Crease, T.J., Tang, H., Lucas, S.M., Robertson, H.M., Bork, P., Koonin, E.V., Zdobnov, E.M., Grigoriev, I.V., Lynch, M. & Boore, J.L.
Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761. Europe PMC

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., Jensen, L.J. & von Mering, C.
Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. Epub 2010 Nov 2. Europe PMC

Network neighbors of drug targets contribute to drug side-effect similarity.
Brouwers, L., Iskar, M., Zeller, G., van Noort, V. & Bork, P.
PLoS One. 2011;6(7):e22187. Epub 2011 Jul 13. Europe PMC

SmashCell: a software framework for the analysis of single-cell amplified genome sequences.
Harrington, E.D., Arumugam, M., Raes, J., Bork, P. & Relman, D.A.
Bioinformatics. 2010 Dec 1;26(23):2979-80. Epub 2010 Oct 21. Europe PMC

SmashCommunity: a metagenomic annotation and analysis tool.
Arumugam, M., Harrington, E.D., Foerstner, K.U., Raes, J. & Bork, P.
Bioinformatics. 2010 Dec 1;26(23):2977-8. Epub 2010 Oct 19. Europe PMC

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.
Gallego, O., Betts, M.J., Gvozdenovic-Jeremic, J., Maeda, K., Matetzki, C., Aguilar-Gurrieri, C., Beltran-Alvarez, P., Bonn, S., Fernandez-Tornero, C., Jensen, L.J., Kuhn, M., Trott, J., Rybin, V., Muller, C.W., Bork, P., Kaksonen, M., Russell, R.B. & Gavin, A.C.
Mol Syst Biol. 2010 Nov 30;6:430. doi: 10.1038/msb.2010.87. Europe PMC

A human gut microbial gene catalogue established by metagenomic sequencing.
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D.R., Li, J., Xu, J., Li, S., Li, D., Cao, J., Wang, B., Liang, H., Zheng, H., Xie, Y., Tap, J., Lepage, P., Bertalan, M., Batto, J.M., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H.B., Pelletier, E., Renault, P., Sicheritz-Ponten, T., Turner, K., Zhu, H., Yu, C., Li, S., Jian, M., Zhou, Y., Li, Y., Zhang, X., Li, S., Qin, N., Yang, H., Wang, J., Brunak, S., Dore, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., Bork, P., Ehrlich, S.D. & Wang, J.
Nature. 2010 Mar 4;464(7285):59-65. Europe PMC

High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
Granovskaia, M.V., Jensen, L.J., Ritchie, M.E., Toedling, J., Ning, Y., Bork, P., Huber, W. & Steinmetz, L.M.
Genome Biol. 2010 Mar 1;11(3):R24. Europe PMC

Evolution and regulation of cellular periodic processes: a role for paralogues.
Trachana, K., Jensen, L.J. & Bork, P.
EMBO Rep. 2010 Mar;11(3):233-8. Epub 2010 Feb 19. Europe PMC

Ancient animal microRNAs and the evolution of tissue identity.
Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., Snyman, H., Hannon, G.J., Bork, P. & Arendt, D.
Nature. 2010 Feb 25;463(7284):1084-8. Epub 2010 Jan 31. Europe PMC

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.
Werren, J.H., Richards, S., Desjardins, C.A., Niehuis, O., Gadau, J., Colbourne, J.K., Werren, J.H., Richards, S., Desjardins, C.A., Niehuis, O., Gadau, J., Colbourne, J.K., Beukeboom, L.W., Desplan, C., Elsik, C.G., Grimmelikhuijzen, C.J., Kitts, P., Lynch, J.A., Murphy, T., Oliveira, D.C., Smith, C.D., van de Zande, L., Worley, K.C., Zdobnov, E.M., Aerts, M., Albert, S., Anaya, V.H., Anzola, J.M., Barchuk, A.R., Behura, S.K., Bera, A.N., Berenbaum, M.R., Bertossa, R.C., Bitondi, M.M., Bordenstein, S.R., Bork, P., Bornberg-Bauer, E., Brunain, M., Cazzamali, G., Chaboub, L., Chacko, J., Chavez, D., Childers, C.P., Choi, J.H., Clark, M.E., Claudianos, C., Clinton, R.A., Cree, A.G., Cristino, A.S., Dang, P.M., Darby, A.C., de Graaf, D.C., Devreese, B., Dinh, H.H., Edwards, R., Elango, N., Elhaik, E., Ermolaeva, O., Evans, J.D., Foret, S., Fowler, G.R., Gerlach, D., Gibson, J.D., Gilbert, D.G., Graur, D., Grunder, S., Hagen, D.E., Han, Y., Hauser, F., Hultmark, D., Hunter HC, 4th, Hurst, G.D., Jhangian, S.N., Jiang, H., Johnson, R.M., Jones, A.K., Junier, T., Kadowaki, T., Kamping, A., Kapustin, Y., Kechavarzi, B., Kim, J., Kim, J., Kiryutin, B., Koevoets, T., Kovar, C.L., Kriventseva, E.V., Kucharski, R., Lee, H., Lee, S.L., Lees, K., Lewis, L.R., Loehlin, D.W., Logsdon JM, J.r, Lopez, J.A., Lozado, R.J., Maglott, D., Maleszka, R., Mayampurath, A., Mazur, D.J., McClure, M.A., Moore, A.D., Morgan, M.B., Muller, J., Munoz-Torres, M.C., Muzny, D.M., Nazareth, L.V., Neupert, S., Nguyen, N.B., Nunes, F.M., Oakeshott, J.G., Okwuonu, G.O., Pannebakker, B.A., Pejaver, V.R., Peng, Z., Pratt, S.C., Predel, R., Pu, L.L., Ranson, H., Raychoudhury, R., Rechtsteiner, A., Reese, J.T., Reid, J.G., Riddle, M., Robertson, H.M., Romero-Severson, J., Rosenberg, M., Sackton, T.B., Sattelle, D.B., Schluns, H., Schmitt, T., Schneider, M., Schuler, A., Schurko, A.M., Shuker, D.M., Simoes, Z.L., Sinha, S., Smith, Z., Solovyev, V., Souvorov, A., Springauf, A., Stafflinger, E., Stage, D.E., Stanke, M., Tanaka, Y., Telschow, A., Trent, C., Vattathil, S., Verhulst, E.C., Viljakainen, L., Wanner, K.W., Waterhouse, R.M., Whitfield, J.B., Wilkes, T.E., Williamson, M., Willis, J.H., Wolschin, F., Wyder, S., Yamada, T., Yi, S.V., Zecher, C.N., Zhang, L. & Gibbs, R.A.
Science. 2010 Jan 15;327(5963):343-8. Europe PMC

AQUA: automated quality improvement for multiple sequence alignments.
Muller, J., Creevey, C.J., Thompson, J.D., Arendt, D. & Bork, P.
Bioinformatics. 2010 Jan 15;26(2):263-5. Epub 2009 Nov 19. Europe PMC

Drug-induced regulation of target expression.
Iskar, M., Campillos, M., Kuhn, M., Jensen, L.J., van Noort, V. & Bork, P.
PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000925. Europe PMC

Impact of genome reduction on bacterial metabolism and its regulation.
Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.H., Wodke, J.A., Guell, M., Martinez, S., Bourgeois, R., Kuhner, S., Raineri, E., Letunic, I., Kalinina, O.V., Rode, M., Herrmann, R., Gutierrez-Gallego, R., Russell, R.B., Gavin, A.C., Bork, P. & Serrano, L.
Science. 2009 Nov 27;326(5957):1263-8. Europe PMC

Transcriptome complexity in a genome-reduced bacterium.
Guell, M., van Noort, V., Yus, E., Chen, W.H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kuhner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A.C., Bork, P. & Serrano, L.
Science. 2009 Nov 27;326(5957):1268-71. Europe PMC

Evolution of biomolecular networks: lessons from metabolic and protein interactions.
Yamada, T. & Bork, P.
Nat Rev Mol Cell Biol. 2009 Nov;10(11):791-803. Europe PMC

ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny, G., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Riethoven, J.J., Nardone, F., Stanley, E., Fallsehr, C., Hofmann, O., Kull, M., Harrington, E., Boue, S., Eyras, E., Plass, M., Lopez, F., Ritchie, W., Moucadel, V., Ara, T., Pospisil, H., Herrmann, A., G Reich, J., Guigo, R., Bork, P., Doeberitz, M.K., Vilo, J., Hide, W., Apweiler, R., Thanaraj, T.A. & Gautheret, D.
Genomics. 2009 Mar;93(3):213-20. Epub 2008 Dec 24. Europe PMC

Quantifying environmental adaptation of metabolic pathways in metagenomics.
Gianoulis, T.A., Raes, J., Patel, P.V., Bjornson, R., Korbel, J.O., Letunic, I., Yamada, T., Paccanaro, A., Jensen, L.J., Snyder, M., Bork, P. & Gerstein, M.B.
Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1374-9. Epub 2009 Jan 22. Europe PMC

Sequence-based feature prediction and annotation of proteins.
Juncker, A.S., Jensen, L.J., Pierleoni, A., Bernsel, A., Tress, M.L., Bork, P., von Heijne, G., Valencia, A., Ouzounis, C.A., Casadio, R. & Brunak, S.
Genome Biol. 2009 Feb 2;10(2):206. Europe PMC

SMART 6: recent updates and new developments.
Letunic, I., Doerks, T. & Bork, P.
Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32. Epub 2008 Oct 31. Europe PMC

InterPro: the integrative protein signature database.
Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. & Yeats, C.
Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. Epub 2008 Oct 21. Europe PMC

Proteome organization in a genome-reduced bacterium.
Kuhner, S., van Noort, V., Betts, M.J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., Castano-Diez, D., Chen, W.H., Devos, D., Guell, M., Norambuena, T., Racke, I., Rybin, V., Schmidt, A., Yus, E., Aebersold, R., Herrmann, R., Bottcher, B., Frangakis, A.S., Russell, R.B., Serrano, L., Bork, P. & Gavin, A.C.
Science. 2009 Nov 27;326(5957):1235-40. doi: 10.1126/science.1176343.
Full text Europe PMC

Molecular eco-systems biology: towards an understanding of community function.
Raes, J. & Bork, P.
Nat Rev Microbiol. 2008 Sep;6(9):693-9. Epub 2008 Jun 30. Europe PMC

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.
Pincus, D., Letunic, I., Bork, P. & Lim, W.A.
Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9680-4. Epub 2008 Jul 3. Europe PMC

Drug target identification using side-effect similarity.
Campillos, M., Kuhn, M., Gavin, A.C., Jensen, L.J. & Bork, P.
Science. 2008 Jul 11;321(5886):263-6. Europe PMC

KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S. & Kanehisa, M.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W423-6. Epub 2008 May13. Europe PMC

iPath: interactive exploration of biochemical pathways and networks.
Letunic, I., Yamada, T., Kanehisa, M. & Bork, P.
Trends Biochem Sci. 2008 Mar;33(3):101-3. doi: 10.1016/j.tibs.2008.01.001. Epub2008 Feb 13. Europe PMC

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
King, N., Westbrook, M.J., Young, S.L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., Marr, M., Pincus, D., Putnam, N., Rokas, A., Wright, K.J., Zuzow, R., Dirks, W., Good, M., Goodstein, D., Lemons, D., Li, W., Lyons, J.B., Morris, A., Nichols, S., Richter, D.J., Salamov, A., Sequencing, J.G., Bork, P., Lim, W.A., Manning, G., Miller, W.T., McGinnis, W., Shapiro, H., Tjian, R., Grigoriev, I.V. & Rokhsar, D.
Nature. 2008 Feb 14;451(7180):783-8. Europe PMC

4DXpress: a database for cross-species expression pattern comparisons.
Haudry, Y., Berube, H., Letunic, I., Weeber, P.D., Gagneur, J., Girardot, C., Kapushesky, M., Arendt, D., Bork, P., Brazma, A., Furlong, E.E., Wittbrodt, J. & Henrich, T.
Nucleic Acids Res. 2008 Jan;36(Database issue):D847-53. Epub 2007 Oct 4. Europe PMC

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families.
Shah, P.K., Tripathi, L.P., Jensen, L.J., Gahnim, M., Mason, C., Furlong, E.E., Rodrigues, V., White, K.P., Bork, P. & Sowdhamini, R.
Gene. 2008 Jan 15;407(1-2):199-215. Epub 2007 Oct 15. Europe PMC

NetworKIN: a resource for exploring cellular phosphorylation networks.
Linding, R., Jensen, L.J., Pasculescu, A., Olhovsky, M., Colwill, K., Bork, P., Yaffe, M.B. & Pawson, T.
Nucleic Acids Res. 2008 Jan;36(Database issue):D695-9. Epub 2007 Nov 2. Europe PMC

STITCH: interaction networks of chemicals and proteins.
Kuhn, M., von Mering, C., Campillos, M., Jensen, L.J. & Bork, P.
Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8. Epub 2007 Dec 15. Europe PMC

eggNOG: automated construction and annotation of orthologous groups of genes.
Jensen, L.J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. & Bork, P.
Nucleic Acids Res. 2008 Jan;36(Database issue):D250-4. Epub 2007 Oct 16. Europe PMC

SuperTarget and Matador: resources for exploring drug-target relationships.
Gunther, S., Kuhn, M., Dunkel, M., Campillos, M., Senger, C., Petsalaki, E., Ahmed, J., Urdiales, E.G., Gewiess, A., Jensen, L.J., Schneider, R., Skoblo, R., Russell, R.B., Bourne, P.E., Bork, P. & Preissner, R.
Nucleic Acids Res. 2008 Jan;36(Database issue):D919-22. Epub 2007 Oct 16. Europe PMC

Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.
Quijano, C., Tomancak, P., Lopez-Marti, J., Suyama, M., Bork, P., Milan, M., Torrents, D. & Manzanares, M.
Genome Biol. 2008;9(12):R176. Epub 2008 Dec 16. Europe PMC

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
Palleja, A., Harrington, E.D. & Bork, P.
BMC Genomics. 2008 Jul 15;9:335. Europe PMC

Linear motif atlas for phosphorylation-dependent signaling.
Miller, M.L., Jensen, L.J., Diella, F., Jorgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S.A., Bordeaux, J., Sicheritz-Ponten, T., Olhovsky, M., Pasculescu, A., Alexander, J., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., Turk, B.E., Yaffe, M.B., Brunak, S. & Linding, R.
Sci Signal. 2008 Sep 2;1(35):ra2. Europe PMC

Circular reasoning rather than cyclic expression.
Jensen, L.J., de Lichtenberg, U., Jensen, T.S., Brunak, S. & Bork, P.
Genome Biol. 2008;9(6):403. Epub 2008 Jun 23. Europe PMC

A nitrile hydratase in the eukaryote Monosiga brevicollis.
Foerstner, K.U., Doerks, T., Muller, J., Raes, J. & Bork, P.
PLoS One. 2008;3(12):e3976. Epub 2008 Dec 19. Europe PMC

Genome-wide experimental determination of barriers to horizontal gene transfer.
Sorek, R., Zhu, Y., Creevey, C.J., Francino, M.P., Bork, P. & Rubin, E.M.
Science. 2007 Nov 30;318(5855):1449-52. Epub 2007 Oct 18. Europe PMC

Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.
Eulalio, A., Rehwinkel, J., Stricker, M., Huntzinger, E., Yang, S.F., Doerks, T., Dorner, S., Bork, P., Boutros, M. & Izaurralde, E.
Genes Dev. 2007 Oct 15;21(20):2558-70. Epub 2007 Sep 27. Europe PMC

Get the most out of your metagenome: computational analysis of environmental sequence data.
Raes, J., Foerstner, K.U. & Bork, P.
Curr Opin Microbiol. 2007 Oct;10(5):490-8. Epub 2007 Oct 23. Europe PMC

Quantitative assessment of protein function prediction from metagenomics shotgun sequences.
Harrington, E.D., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., Raes, J. & Bork, P.
Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13913-8. Epub 2007 Aug 23. Europe PMC

Evolution of cell cycle control: same molecular machines, different regulation.
de Lichtenberg, U., Jensen, T.S., Brunak, S., Bork, P. & Jensen, L.J.
Cell Cycle. 2007 Aug 1;6(15):1819-25. Epub 2007 Jun 4. Europe PMC

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
Pachkov, M., Dandekar, T., Korbel, J., Bork, P. & Schuster, S.
Gene. 2007 Jul 15;396(2):215-25. Epub 2007 Mar 24. Europe PMC

Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals.
Danckwardt, S., Kaufmann, I., Gentzel, M., Foerstner, K.U., Gantzert, A.S., Gehring, N.H., Neu-Yilik, G., Bork, P., Keller, W., Wilm, M., Hentze, M.W. & Kulozik, A.E.
EMBO J. 2007 Jun 6;26(11):2658-69. Epub 2007 Apr 26. Europe PMC

Systematic discovery of in vivo phosphorylation networks.
Linding, R., Jensen, L.J., Ostheimer, G.J., van Vugt, M.A., Jorgensen, C., Miron, I.M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J.G., Samson, L.D., Woodgett, J.R., Russell, R.B., Bork, P., Yaffe, M.B. & Pawson, T.
Cell. 2007 Jun 29;129(7):1415-26. Epub 2007 Jun 14. Europe PMC

Protein function space: viewing the limits or limited by our view?
Raes, J., Harrington, E.D., Singh, A.H. & Bork, P.
Curr Opin Struct Biol. 2007 Jun;17(3):362-9. Epub 2007 Jun 15. Europe PMC

Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes.
Boettner, M., Steffens, C., von Mering, C., Bork, P., Stahl, U. & Lang, C.
J Biotechnol. 2007 May 31;130(1):1-10. Epub 2007 Feb 28. Europe PMC

Quantitative phylogenetic assessment of microbial communities in diverse environments.
von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., Ward, N. & Bork, P.
Science. 2007 Feb 23;315(5815):1126-30. Epub 2007 Feb 1. Europe PMC

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Letunic, I. & Bork, P.
Bioinformatics. 2007 Jan 1;23(1):127-8. Epub 2006 Oct 18. Europe PMC

Quantification of insect genome divergence.
Zdobnov, E.M. & Bork, P.
Trends Genet. 2007 Jan;23(1):16-20. Epub 2006 Nov 9. Europe PMC

STRING 7--recent developments in the integration and prediction of protein interactions.
von Mering, C., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B. & Bork, P.
Nucleic Acids Res. 2007 Jan;35(Database issue):D358-62. Epub 2006 Nov 10. Europe PMC

New developments in the InterPro database.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevaux, P.S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J.D., Sigrist, C.J., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. & Yeats, C.
Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8. Europe PMC

Prediction of effective genome size in metagenomic samples.
Raes, J., Korbel, J.O., Lercher, M.J., von Mering, C. & Bork, P.
Genome Biol. 2007;8(1):R10. Europe PMC

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
Hooper, S.D., Boue, S., Krause, R., Jensen, L.J., Mason, C.E., Ghanim, M., White, K.P., Furlong, E.E. & Bork, P.
Mol Syst Biol. 2007;3:72. Epub 2007 Jan 16. Europe PMC

Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome.
Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D. & Arnone, M.I.
Dev Biol. 2006 Dec 1;300(1):461-75. Epub 2006 Sep 5. Europe PMC

Computational characterization of multiple Gag-like human proteins.
Campillos, M., Doerks, T., Shah, P.K. & Bork, P.
Trends Genet. 2006 Nov;22(11):585-9. Epub 2006 Sep 18. Europe PMC

Co-evolution of transcriptional and post-translational cell-cycle regulation.
Jensen, L.J., Jensen, T.S., de Lichtenberg, U., Brunak, S. & Bork, P.
Nature. 2006 Oct 5;443(7111):594-7. Epub 2006 Sep 27. Europe PMC

Assessing systems properties of yeast mitochondria through an interaction map of the organelle.
Perocchi, F., Jensen, L.J., Gagneur, J., Ahting, U., von Mering, C., Bork, P., Prokisch, H. & Steinmetz, L.M.
PLoS Genet. 2006 Oct 20;2(10):e170. Europe PMC

mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.
Behm-Ansmant, I., Rehwinkel, J., Doerks, T., Stark, A., Bork, P. & Izaurralde, E.
Genes Dev. 2006 Jul 15;20(14):1885-98. Epub 2006 Jun 30. Europe PMC

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Suyama, M., Torrents, D. & Bork, P.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12. Europe PMC

A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development.
Sandmann, T., Jensen, L.J., Jakobsen, J.S., Karzynski, M.M., Eichenlaub, M.P., Bork, P. & Furlong, E.E.
Dev Cell. 2006 Jun;10(6):797-807. Europe PMC

LSAT: learning about alternative transcripts in MEDLINE.
Shah, P.K. & Bork, P.
Bioinformatics. 2006 Apr 1;22(7):857-65. Epub 2006 Jan 12. Europe PMC

Proteome survey reveals modularity of the yeast cell machinery.
Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Dumpelfeld, B., Edelmann, A., Heurtier, M.A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A.M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J.M., Kuster, B., Bork, P., Russell, R.B. & Superti-Furga, G.
Nature. 2006 Mar 30;440(7084):631-6. Epub 2006 Jan 22. Europe PMC

Toward automatic reconstruction of a highly resolved tree of life.
Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, C.J., Snel, B. & Bork, P.
Science. 2006 Mar 3;311(5765):1283-7. Europe PMC

Comparative analysis of environmental sequences: potential and challenges.
Förstner, K.U., von Mering, C. & Bork, P.
Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):519-23. Europe PMC

Extraction of regulatory gene/protein networks from Medline.
Saric, J., Jensen, L.J., Ouzounova, R., Rojas, I. & Bork, P.
Bioinformatics. 2006 Mar 15;22(6):645-50. Epub 2005 Jul 26. Europe PMC

Similar gene expression profiles do not imply similar tissue functions.
Yanai, I., Korbel, J.O., Boue, S., McWeeney, S.K., Bork, P. & Lercher, M.J.
Trends Genet. 2006 Mar;22(3):132-8. Epub 2006 Feb 9. Europe PMC

Identification and analysis of evolutionarily cohesive functional modules in protein networks.
Campillos, M., von Mering, C., Jensen, L.J. & Bork, P.
Genome Res. 2006 Mar;16(3):374-82. Epub 2006 Jan 31. Europe PMC

Literature mining for the biologist: from information retrieval to biological discovery.
Jensen, L.J., Saric, J. & Bork, P.
Nat Rev Genet. 2006 Feb;7(2):119-29. Europe PMC

SMART 5: domains in the context of genomes and networks.
Letunic, I., Copley, R.R., Pils, B., Pinkert, S., Schultz, J. & Bork, P.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D257-60. Europe PMC

Insights into social insects from the genome of the honeybee Apis mellifera.
Sequencing Consortium, T.H. (Bork, P.)
Nature. 2006 Oct 26;443(7114):931-49. Europe PMC

Medusa: a simple tool for interaction graph analysis.
Hooper, S.D. & Bork, P.
Bioinformatics. 2005 Dec 15;21(24):4432-3. Epub 2005 Sep 27. Europe PMC

Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases.
Mees, A., Rock, R., Ciccarelli, F.D., Leberfinger, C.B., Borawski, J.M., Bork, P., Wiese, S., Gessler, M. & Kerkhoff, E.
Gene Expr Patterns. 2005 Dec;6(1):79-85. Epub 2005 Aug 15. Europe PMC

Environments shape the nucleotide composition of genomes.
Foerstner, K.U., von Mering, C., Hooper, S.D. & Bork, P.
EMBO Rep 2005 Dec;6(12):1208-13. Europe PMC

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii.
Raible, F., Tessmar-Raible, K., Osoegawa, K., Wincker, P., Jubin, C., Balavoine, G., Ferrier, D., Benes, V., de Jong, P., Weissenbach, J., Bork, P. & Arendt, D.
Science 2005 Nov 25;310(5752):1325-6. Europe PMC

Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.
Taxis, C., Keller, P., Kavagiou, Z., Jensen, L.J., Colombelli, J., Bork, P., Stelzer, E.H.K. & Knop, M.
J Cell Biol 2005 Nov 21;171(4):627-40. Epub 2005 Nov 14. Europe PMC

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.
Suyama, M., Lathe WC, 3rd & Bork, P.
FEBS Lett 2005 Oct 10;579(24):5281-6. Europe PMC

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.
Rehwinkel, J., Letunic, I., Raes, J., Bork, P. & Izaurralde, E.
RNA 2005 Oct;11(10):1530-44. Europe PMC

G2D: a tool for mining genes associated with disease.
Perez-Iratxeta, C., Wjst, M., Bork, P. & Andrade, M.A.
BMC Genet 2005 Aug 22;6:45. Europe PMC

Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones.
Bussow, K., Scheich, C., Sievert, V., Harttig, U., Schultz, J., Simon, B., Bork, P., Lehrach, H. & Heinemann, U.
Microb Cell Fact 2005 Jul 5;4:21. Europe PMC

DCD - a novel plant specific domain in proteins involved in development and programmed cell death.
Tenhaken, R., Doerks, T. & Bork, P.
BMC Bioinformatics 2005 Jul 11;6:169. Europe PMC

Consistency of genome-based methods in measuring Metazoan evolution.
Zdobnov, E.M., von Mering, C., Letunic, I. & Bork, P.
FEBS Lett 2005 Jun 13;579(15):3355-61. Epub 2005 Apr 18. Europe PMC

Extraction of transcript diversity from scientific literature.
Shah, P.K., Jensen, L.J., Boue, S. & Bork, P.
PLoS Comput Biol. 2005 Jun;1(1):e10. Epub 2005 Jun 24. Europe PMC

Is there biological research beyond Systems Biology? A comparative analysis of terms.
Bork, P.
Mol Syst Biol. 2005;1:2005.0012. Epub 2005 May 25. Europe PMC

Towards cellular systems in 4D.
Bork, P. & Serrano, L.
Cell 2005 May 20;121(4):507-9. Europe PMC

Structural similarity to bridge sequence space: finding new families on the bridges.
Shah, P.K., Aloy, P., Bork, P. & Russell, R.B.
Protein Sci 2005 May;14(5):1305-14. Europe PMC

Comparison of computational methods for the identification of cell cycle-regulated genes.
de Lichtenberg, U., Jensen, L.J., Fausboll, A., Jensen, T.S., Bork, P. & Brunak, S.
Bioinformatics. 2005 Apr 1;21(7):1164-71. Epub 2004 Oct 28. Europe PMC

Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
Hillier, L.W., Graves, T.A., Fulton, R.S., Fulton, L.A., Pepin, K.H., Minx, P., Wagner-McPherson, C., Layman, D., Wylie, K., Sekhon, M., Becker, M.C., Fewell, G.A., Delehaunty, K.D., Miner, T.L., Nash, W.E., Kremitzki, C., Oddy, L., Du, H., Sun, H., Bradshaw-Cordum, H., Ali, J., Carter, J., Cordes, M., Harris, A., Isak, A., van Brunt, A., Nguyen, C., Du, F., Courtney, L., Kalicki, J., Ozersky, P., Abbott, S., Armstrong, J., Belter, E.A., Caruso, L., Cedroni, M., Cotton, M., Davidson, T., Desai, A., Elliott, G., Erb, T., Fronick, C., Gaige, T., Haakenson, W., Haglund, K., Holmes, A., Harkins, R., Kim, K., Kruchowski, S.S., Strong, C.M., Grewal, N., Goyea, E., Hou, S., Levy, A., Martinka, S., Mead, K., McLellan, M.D., Meyer, R., Randall-Maher, J., Tomlinson, C., Dauphin-Kohlberg, S., Kozlowicz-Reilly, A., Shah, N., Swearengen-Shahid, S., Snider, J., Strong, J.T., Thompson, J., Yoakum, M., Leonard, S., Pearman, C., Trani, L., Radionenko, M., Waligorski, J.E., Wang, C., Rock, S.M., Tin-Wollam, A.M., Maupin, R., Latreille, P., Wendl, M.C., Yang, S.P., Pohl, C., Wallis, J.W., Spieth, J., Bieri, T.A., Berkowicz, N., Nelson, J.O., Osborne, J., Ding, L., Meyer, R., Sabo, A., Shotland, Y., Sinha, P., Wohldmann, P.E., Cook, L.L., Hickenbotham, M.T., Eldred, J., Williams, D., Jones, T.A., She, X., Ciccarelli, F.D., Izaurralde, E., Taylor, J., Schmutz, J., Myers, R.M., Cox, D.R., Huang, X., McPherson, J.D., Mardis, E.R., Clifton, S.W., Warren, W.C., Chinwalla, A.T., Eddy, S.R., Marra, M.A., Ovcharenko, I., Furey, T.S., Miller, W., Eichler, E.E., Bork, P., Suyama, M., Torrents, D., Waterston, R.H. & Wilson, R.K.
Nature 2005 Apr 7;434(7034):724-31. Europe PMC

Systematic association of genes to phenotypes by genome and literature mining.
Korbel, J.O., Doerks, T., Jensen, L.J., Perez-Iratxeta, C., Kaczanowski, S., Hooper, S.D., Andrade, M.A. & Bork, P.
PLoS Biol 2005 Apr 5;3(5):e134. Europe PMC

Comparative metagenomics of microbial communities.
Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P. & Rubin, E.M.
Science 2005 Apr 22;308(5721):554-7. Europe PMC

The WHy domain mediates the response to desiccation in plants and bacteria.
Ciccarelli, F.D. & Bork, P.
Bioinformatics 2005 Apr 15;21(8):1304-7. Epub 2004 Dec 14. Europe PMC

Complex genomic rearrangements lead to novel primate gene function.
Ciccarelli, F.D., von Mering, C., Suyama, M., Harrington, E.D., Izaurralde, E. & Bork, P.
Genome Res 2005 Mar;15(3):343-51. Epub 2005 Feb 14. Europe PMC

Dynamic complex formation during the yeast cell cycle.
de Lichtenberg, U., Jensen, L.J., Brunak, S. & Bork, P.
Science 2005 Feb 4;307(5710):724-7. Europe PMC

STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. & Bork, P.
Nucleic Acids Res 2005 Jan 1;33 Database Issue:D433-7. Europe PMC

InterPro, progress and status in 2005.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Pagni, M., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J., Silventoinen, V., Studholme, D.J., Vaughan, R. & Wu, C.H.
Nucleic Acids Res 2005 Jan 1;33(Database issue):D201-5. Europe PMC

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
Bourque, G., Zdobnov, E.M., Bork, P., Pevzner, P.A. & Tesler, G.
Genome Res 2005 Jan;15(1):98-110. Epub 2004 Dec 08. Europe PMC

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
Zdobnov, E.M., Campillos, M., Harrington, E.D., Torrents, D. & Bork, P.
Nucleic Acids Res 2005 Feb 16;33(3):946-54. Print 2005. Europe PMC

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Hillier, L.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A., Delany, M.E., Dodgson, J.B., Chinwalla, A.T., Cliften, P.F., Clifton, S.W., Delehaunty, K.D., Fronick, C., Fulton, R.S., Graves, T.A., Kremitzki, C., Layman, D., Magrini, V., McPherson, J.D., Miner, T.L., Minx, P., Nash, W.E., Nhan, M.N., Nelson, J.O., Oddy, L.G., Pohl, C.S., Randall-Maher, J., Smith, S.M., Wallis, J.W., Yang, S.P., Romanov, M.N., Rondelli, C.M., Paton, B., Smith, J., Morrice, D., Daniels, L., Tempest, H.G., Robertson, L., Masabanda, J.S., Griffin, D.K., Vignal, A., Fillon, V., Jacobbson, L., Kerje, S., Andersson, L., Crooijmans, R.P., Aerts, J., van der Poel, J.J., Ellegren, H., Caldwell, R.B., Hubbard, S.J., Grafham, D.V., Kierzek, A.M., McLaren, S.R., Overton, I.M., Arakawa, H., Beattie, K.J., Bezzubov, Y., Boardman, P.E., Bonfield, J.K., Croning, M.D., Davies, R.M., Francis, M.D., Humphray, S.J., Scott, C.E., Taylor, R.G., Tickle, C., Brown, W.R., Rogers, J., Buerstedde, J.M., Wilson, S.A., Stubbs, L., Ovcharenko, I., Gordon, L., Lucas, S., Miller, M.M., Inoko, H., Shiina, T., Kaufman, J., Salomonsen, J., Skjoedt, K., Wong, G.K., Wang, J., Liu, B., Wang, J., Yu, J., Yang, H., Nefedov, M., Koriabine, M., Dejong, P.J., Goodstadt, L., Webber, C., Dickens, N.J., Letunic, I., Suyama, M., Torrents, D., von Mering, C., Zdobnov, E.M., Makova, K., Nekrutenko, A., Elnitski, L., Eswara, P., King, D.C., Yang, S., Tyekucheva, S., Radakrishnan, A., Harris, R.S., Chiaromonte, F., Taylor, J., He, J., Rijnkels, M., Griffiths-Jones, S., Ureta-Vidal, A., Hoffman, M.M., Severin, J., Searle, S.M., Law, A.S., Speed, D., Waddington, D., Cheng, Z., Tuzun, E., Eichler, E., Bao, Z., Flicek, P., Shteynberg, D.D., Brent, M.R., Bye, J.M., Huckle, E.J., Chatterji, S., Dewey, C., Pachter, L., Kouranov, A., Mourelatos, Z., Hatzigeorgiou, A.G., Paterson, A.H., Ivarie, R., Brandstrom, M., Axelsson, E., Backstrom, N., Berlin, S., Webster, M.T., Pourquie, O., Reymond, A., Ucla, C., Antonarakis, S.E., Long, M., Emerson, J.J., Betran, E., Dupanloup, I., Kaessmann, H., Hinrichs, A.S., Bejerano, G., Furey, T.S., Harte, R.A., Raney, B., Siepel, A., Kent, W.J., Haussler, D., Eyras, E., Castelo, R., Abril, J.F., Castellano, S., Camara, F., Parra, G., Guigo, R., Bourque, G., Tesler, G., Pevzner, P.A., Smit, A., Fulton, L.A., Mardis, E.R. & Wilson, R.K.
Nature 2004 Dec 9;432(7018):695-716. Europe PMC

Shared components of protein complexes--versatile building blocks or biochemical artefacts?
Krause, R., von Mering, C., Bork, P. & Dandekar, T.
Bioessays 2004 Dec;26(12):1333-43. Europe PMC

Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression.
Koehl, A., Schmidt, N., Rieger, A., Pilgram, S.M., Letunic, I., Bork, P., Soto, F., Friauf, E. & Nothwang, H.G.
Eur J Neurosci 2004 Dec;20(12):3244-58. Europe PMC

Estimating rates of alternative splicing in mammals and invertebrates.
Kim, H., Klein, R., Majewski, J. & Ott, J.
Nat Genet. 2004 Sep;36(9):915-6; author reply 916-7. Europe PMC

Gene annotation from scientific literature using mappings between keyword systems.
Perez, A.J., Perez-Iratxeta, C., Bork, P., Thode, G. & Andrade, M.A.
Bioinformatics 2004 Sep 1;20(13):2084-91. Epub 2004 Apr 01. Europe PMC

Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome.
Liska, A.J., Popov, A.V., Sunyaev, S., Coughlin, P., Habermann, B., Shevchenko, A., Bork, P., Karsenti, E. & Shevchenko, A.
Proteomics 2004 Sep;4(9):2707-21. Europe PMC

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Suyama, M., Torrents, D. & Bork, P.
Bioinformatics. 2004 Aug 12;20(12):1968-70. Epub 2004 Mar 22. Europe PMC

ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Jensen, L.J., Lagarde, J., von Mering, C. & Bork, P.
Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W445-8. Europe PMC

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
Korbel, J.O., Jensen, L.J., von Mering, C. & Bork, P.
Nat Biotechnol 2004 Jul;22(7):911-7. Europe PMC

Protein interaction networks from yeast to human.
Bork, P., Jensen, L.J., von Mering, C., Ramani, A.K., Lee, I. & Marcotte, E.M.
Curr Opin Struct Biol 2004 Jun;14(3):292-9. Europe PMC

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs, R.A., Weinstock, G.M., Metzker, M.L., Muzny, D.M., Sodergren, E.J., Scherer, S., Scott, G., Steffen, D., Worley, K.C., Burch, P.E., Okwuonu, G., Hines, S., Lewis, L., DeRamo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R., Celera, Holt, R.A., Adams, M.D., Amanatides, P.G., Baden-Tillson, H., Barnstead, M., Chin, S., Evans, C.A., Ferriera, S., Fosler, C., Glodek, A., Gu, Z., Jennings, D., Kraft, C.L., Nguyen, T., Pfannkoch, C.M., Sitter, C., Sutton, G.G., Venter, J.C., Woodage, T., Smith, D., Lee, H.M., Gustafson, E., Cahill, P., Kana, A., Doucette-Stamm, L., Weinstock, K., Fechtel, K., Weiss, R.B., Dunn, D.M., Green, E.D., Blakesley, R.W., Bouffard, G.G., De Jong, P.J., Osoegawa, K., Zhu, B., Marra, M., Schein, J., Bosdet, I., Fjell, C., Jones, S., Krzywinski, M., Mathewson, C., Siddiqui, A., Wye, N., McPherson, J., Zhao, S., Fraser, C.M., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, W.C., Havlak, P.H., Chen, R., Durbin, K.J., Egan, A., Ren, Y., Song, X.Z., Li, B., Liu, Y., Qin, X., Cawley, S., Worley, K.C., Cooney, A.J., D'Souza, L.M., Martin, K., Wu, J.Q., Gonzalez-Garay, M.L., Jackson, A.R., Kalafus, K.J., McLeod, M.P., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, D.A., Zhang, Z., Bailey, J.A., Eichler, E.E., Tuzun, E., Birney, E., Mongin, E., Ureta-Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, B.J., Young, J.M., Huang, H., Wang, H., Xing, H., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Mar Alba, M., Abril, J.F., Guigo, R., Smit, A., Dubchak, I., Rubin, E.M., Couronne, O., Poliakov, A., Hubner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y.A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, H.J., Bromberg, S., Gullings-Handley, J., Jensen-Seaman, M.I., Kwitek, A.E., Lazar, J., Pasko, D., Tonellato, P.J., Twigger, S., Ponting, C.P., Duarte, J.M., Rice, S., Goodstadt, L., Beatson, S.A., Emes, R.D., Winter, E.E., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, R.C., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, T.D., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, S.M., Cooper, G.M., Batzoglou, S., Brudno, M., Sidow, A., Stone, E.A., Venter, J.C., Payseur, B.A., Bourque, G., Lopez-Otin, C., Puente, X.S., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, V.B., Caspi, A., Tesler, G., Pevzner, P.A., Haussler, D., Roskin, K.M., Baertsch, R., Clawson, H., Furey, T.S., Hinrichs, A.S., Karolchik, D., Kent, W.J., Rosenbloom, K.R., Trumbower, H., Weirauch, M., Cooper, D.N., Stenson, P.D., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, R.R., Taylor, M.S., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S. & Collins, F.
Nature 2004 Apr 1;428(6982):493-521. Europe PMC

Structure-based assembly of protein complexes in yeast.
Aloy, P., Böttcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A.C., Bork, P., Superti-Furga, G., Serrano, L. & Russell, R.B.
Science 2004 Mar 26;303(5666):2026-9. Europe PMC

Global analysis of bacterial transcription factors to predict cellular target processes.
Doerks, T., Andrade, M.A., Lathe W, 3rd, von Mering, C. & Bork, P.
Trends Genet 2004 Mar;20(3):126-31. Europe PMC

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S.G., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C. & Apweiler, R.
Nat Biotechnol 2004 Feb;22(2):177-83. Europe PMC

RanBP2/Nup358 Provides a Major Binding Site for NXF1-p15 Dimers at the Nuclear Pore Complex and Functions in Nuclear mRNA Export.
Forler, D., Rabut, G., Ciccarelli, F.D., Herold, A., Kocher, T., Niggeweg, R., Bork, P., Ellenberg, J. & Izaurralde, E.
Mol Cell Biol 2004 Feb;24(3):1155-67. Europe PMC

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.H., Gohla, R., Gossling, F., Grote, K., Heidtke, K., Herrmann, A., O'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J.O., Lengauer, T., Liebich, I., Van Der Linden, M., Luz, H., Meissner, K., Von Mering, C., Mevissen, H.T., Mewes, H.W., Michael, H., Mokrejs, M., Muller, T., Pospisil, H., Rarey, M., Reich, J.G., Schneider, R., Schomburg, D., Schulze-Kremer, S., Schwarzer, K., Sommer, I., Springstubbe, S., Suhai, S., Thoppae, G., Vingron, M., Warfsmann, J., Werner, T., Wetzler, D., Wingender, E. & Zimmer, R.
Bioinformatics 2004 Jan 22;20(2):268-270. Europe PMC

SMART 4.0: towards genomic data integration.
Letunic, I., Copley, R.R., Schmidt, S., Ciccarelli, F.D., Doerks, T., Schultz, J., Ponting, C.P. & Bork, P.
Nucleic Acids Res 2004 Jan 1;32(1):D142-4. Europe PMC

Extracting regulatory gene expression networks from pubmed.
Sarik, J., Lensen, L.J., Ouzounova, R., Rojas, I. & Bork, P.
Proceedings of the 42nd annuual meeting of the association of computational linguistics 2004;192-199.

Quality analysis and integration of large scale molecular data sets.
Jensen, L.J. & Bork, P.
Drug Discovery Today (TARGETS) 2004;3:51-56.

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
Doerks, T., von Mering, C. & Bork, P.
Nucleic Acids Res ;32(21):6321-6. Print 2004. Europe PMC

Sequences and topology: Genes and structures in context.
Bork, P. & Orengo, C.
Curr. Opin. Struct. Biol. 2004 14 261-263

Genome evolution reveals biochemical networks and functional modules.
von Mering, C., Zdobnov, E.M., Tsoka, S., Ciccarelli, F.D., Pereira-Leal, J.B., Ouzounis, C.A. & Bork, P.
Proc Natl Acad Sci U S A 2003 Dec 23;100(26):15428-33. Europe PMC

The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
Ciccarelli, F.D., Izaurralde, E. & Bork, P.
BMC Bioinformatics 2003 Dec 19;4(1):64. Europe PMC

Impact of selection, mutation rate and genetic drift on human genetic variation.
Sunyaev, S., Kondrashov, F.A., Bork, P. & Ramensky, V.
Hum Mol Genet 2003 Dec 15;12(24):3325-30. Europe PMC

A genome-wide survey of human pseudogenes.
Torrents, D., Suyama, M., Zdobnov, E. & Bork, P.
Genome Res 2003 Dec;13(12):2559-67. Europe PMC

Protein disorder prediction. Implications for structural proteomics.
Linding, R., Jensen, L.J., Diella, F., Bork, P., Gibson, T.J. & Russell, R.B.
Structure (Camb) 2003 Nov;11(11):1453-9. Europe PMC

Alternative splicing and evolution.
Boue, S., Letunic, I. & Bork, P.
Bioessays 2003 Nov;25(11):1031-4. Europe PMC

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Krause, R., von Mering, C. & Bork, P.
Bioinformatics 2003 Oct 12;19(15):1901-8. Europe PMC

Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways.
Gatfield, D., Unterholzner, L., Ciccarelli, F.D., Bork, P. & Izaurralde, E.
EMBO J 2003 Aug 1;22(15):3960-70. Europe PMC

The DNA sequence of human chromosome 7.
Hillier, L.W., Fulton, R.S., Fulton, L.A., Graves, T.A., Pepin, K.H., Wagner-McPherson, C., Layman, D., Maas, J., Jaeger, S., Walker, R., Wylie, K., Sekhon, M., Becker, M.C., O'Laughlin, M.D., Schaller, M.E., Fewell, G.A., Delehaunty, K.D., Miner, T.L., Nash, W.E., Cordes, M., Du, H., Sun, H., Edwards, J., Bradshaw-Cordum, H., Ali, J., Andrews, S., Isak, A., Vanbrunt, A., Nguyen, C., Du, F., Lamar, B., Courtney, L., Kalicki, J., Ozersky, P., Bielicki, L., Scott, K., Holmes, A., Harkins, R., Harris, A., Strong, C.M., Hou, S., Tomlinson, C., Dauphin-Kohlberg, S., Kozlowicz-Reilly, A., Leonard, S., Rohlfing, T., Rock, S.M., Tin-Wollam, A.M., Abbott, A., Minx, P., Maupin, R., Strowmatt, C., Latreille, P., Miller, N., Johnson, D., Murray, J., Woessner, J.P., Wendl, M.C., Yang, S.P., Schultz, B.R., Wallis, J.W., Spieth, J., Bieri, T.A., Nelson, J.O., Berkowicz, N., Wohldmann, P.E., Cook, L.L., Hickenbotham, M.T., Eldred, J., Williams, D., Bedell, J.A., Mardis, E.R., Clifton, S.W., Chissoe, S.L., Marra, M.A., Raymond, C., Haugen, E., Gillett, W., Zhou, Y., James, R., Phelps, K., Iadanoto, S., Bubb, K., Simms, E., Levy, R., Clendenning, J., Kaul, R., Kent, W.J., Furey, T.S., Baertsch, R.A., Brent, M.R., Keibler, E., Flicek, P., Bork, P., Suyama, M., Bailey, J.A., Portnoy, M.E., Torrents, D., Chinwalla, A.T., Gish, W.R., Eddy, S.R., McPherson, J.D., Olson, M.V., Eichler, E.E., Green, E.D., Waterston, R.H. & Wilson, R.K.
Nature 2003 Jul 10;424(6945):157-64. Europe PMC

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll, P., Linding, R., Gemund, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M., Ausiello, G., Brannetti, B., Costantini, A., Ferre, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, L., Kuster, B., Helmer-Citterich, M., Hunter, W.N., Aasland, R. & Gibson, T.J.
Nucleic Acids Res 2003 Jul 1;31(13):3625-30. Europe PMC

Update on XplorMed: A web server for exploring scientific literature.
Perez-Iratxeta, C., Perez, A.J., Bork, P. & Andrade, M.A.
Nucleic Acids Res 2003 Jul 1;31(13):3866-8. Europe PMC

Systematic discovery of analogous enzymes in thiamin biosynthesis.
Morett, E., Korbel, J.O., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Schmidt, S., Snel, B. & Bork, P.
Nat Biotechnol 2003 Jul;21(7):790-5. Europe PMC

The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold.
Ciccarelli, F.D., Bork, P. & Kerkhoff, E.
Trends Biochem Sci 2003 Jul;28(7):349-52. Europe PMC

Metabolites: a helping hand for pathway evolution?
Schmidt, S., Sunyaev, S., Bork, P. & Dandekar, T.
Trends Biochem Sci 2003 Jun;28(6):336-41. Europe PMC

Information extraction from full text scientific articles: where are the keywords?
Shah, P.K., Perez-Iratxeta, C., Bork, P. & Andrade, M.A.
BMC Bioinformatics 2003 May 29;4(1):20. Europe PMC

The way we write.
Netzel, R., Perez-Iratxeta, C., Bork, P. & Andrade, M.A.
EMBO Rep 2003 May;4(5):446-51. Europe PMC

Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes.
Woerner, S.M., Benner, A., Sutter, C., Schiller, M., Yuan, Y.P., Keller, G., Bork, P., Doeberitz, M.K. & Gebert, J.F.
Oncogene 2003 Apr 17;22(15):2226-35. Europe PMC

Function prediction and protein networks.
Huynen, M.A., Snel, B., Mering, C. & Bork, P.
Curr Opin Cell Biol 2003 Apr;15(2):191-8. Europe PMC

The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia.
Ciccarelli, F.D., Proukakis, C., Patel, H., Cross, H., Azam, S., Patton, M.A., Bork, P. & Crosby, A.H.
Genomics 2003 Apr;81(4):437-41. Europe PMC

Increase of functional diversity by alternative splicing.
Kriventseva, E.V., Koch, I., Apweiler, R., Vingron, M., Bork, P., Gelfand, M.S. & Sunyaev, S.
Trends Genet 2003 Mar;19(3):124-8. Europe PMC

Bioinformatics in the post-sequence era.
Kanehisa, M. & Bork, P.
Nat Genet 2003 Mar;33 Suppl:305-10. Europe PMC

STRING: a database of predicted functional associations between proteins.
von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P. & Snel, B.
Nucleic Acids Res 2003 Jan 1;31(1):258-61. Europe PMC

The InterPro Database, 2003 brings increased coverage and new features.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R.R., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S.E., Pagni, M., Peyruc, D., Ponting, C.P., Selengut, J.D., Servant, F., Sigrist, C.J., Vaughan, R. & Zdobnov, E.M.
Nucleic Acids Res 2003 Jan 1;31(1):315-8. Europe PMC

The human genome: genes, pseudogenes, and variation on chromosome 7.
Waterston, R.H., Hillier, L.W., Fulton, L.A., Fulton, R.S., Graves, T.A., Pepin, K.H., Bork, P., Suyama, M., Torrents, D., Chinwalla, A.T., Mardis, E.R., McPherson, J.D. & Wilson, R.K.
Cold Spring Harb Symp Quant Biol 2003;68:13-22. Europe PMC

Detection and characterization of pseudogenes.
Torrents, D., Suyama, M. & Bork, P.
In "Bioinformatics and Genomes." M. Andrade (Ed). Horizon Sci. Press, 197-209

Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes.
Shevchenko, A., Sunyaev, S., Liska, A., Bork, P. & Shevchenko, A.
Methods Mol Biol 2003;211:221-34. Europe PMC

High rate of gene displacement in vitamine biosynthetic pathways.
Morett, E., Saab-Rincon, G., Merino, E., Bork, P., Rajan, E., Olvera, L. & Olvera, M.
In "Bioinformatics and Genomes." M. Andrade (Ed.). Horizon Sci. Press, 69-79

Initial sequencing and comparative analysis of the mouse genome.
Waterston, R.H., Lindblad-Toh, K., Birney, E., et al.
Nature 2002 Dec 5;420(6915):520-62. Europe PMC

Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes.
Kloor, M., Bork, P., Duwe, A., Klaes, R., von Knebel Doeberitz, M. & Ridder, R.
Biochim Biophys Acta 2002 Dec 12;1579(2-3):219-24. Europe PMC

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.
Zdobnov, E.M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D., Holt, R.A., Subramanian, G.M., Mueller, H.M., Dimopoulos, G., Law, J.H., Wells, M.A., Birney, E., Charlab, R., Halpern, A.L., Kokoza, E., Kraft, C.L., Lai, Z., Lewis, S., Louis, C., Barillas-Mury, C., Nusskern, D., Rubin, G.M., Salzberg, S.L., Sutton, G.G., Topalis, P., Wides, R., Wincker, P., Yandell, M., Collins, F.H., Ribeiro, J., Gelbart, W.M., Kafatos, F.C. & Bork, P.
Science 2002 Oct 4;298(5591):149-59. Europe PMC

The genome sequence of the malaria mosquito Anopheles gambiae.
Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M., Wides, R., Salzberg, S.L., Loftus, B., Yandell, M., Majoros, W.H., Rusch, D.B., Lai, Z., Kraft, C.L., Abril, J.F., Anthouard, V., Arensburger, P., Atkinson, P.W., Baden, H., de Berardinis, V., Baldwin, D., Benes, V., Biedler, J., Blass, C., Bolanos, R., Boscus, D., Barnstead, M., Cai, S., Center, A., Chatuverdi, K., Christophides, G.K., Chrystal, M.A., Clamp, M., Cravchik, A., Curwen, V., Dana, A., Delcher, A., Dew, I., Evans, C.A., Flanigan, M., Grundschober-Freimoser, A., Friedli, L., Gu, Z., Guan, P., Guigo, R., Hillenmeyer, M.E., Hladun, S.L., Hogan, J.R., Hong, Y.S., Hoover, J., Jaillon, O., Ke, Z., Kodira, C., Kokoza, E., Koutsos, A., Letunic, I., Levitsky, A., Liang, Y., Lin, J.J., Lobo, N.F., Lopez, J.R., Malek, J.A., McIntosh, T.C., Meister, S., Miller, J., Mobarry, C., Mongin, E., Murphy, S.D., O'Brochta, D.A., Pfannkoch, C., Qi, R., Regier, M.A., Remington, K., Shao, H., Sharakhova, M.V., Sitter, C.D., Shetty, J., Smith, T.J., Strong, R., Sun, J., Thomasova, D., Ton, L.Q., Topalis, P., Tu, Z., Unger, M.F., Walenz, B., Wang, A., Wang, J., Wang, M., Wang, X., Woodford, K.J., Wortman, J.R., Wu, M., Yao, A., Zdobnov, E.M., Zhang, H., Zhao, Q., Zhao, S., Zhu, S.C., Zhimulev, I., Coluzzi, M., della Torre, A., Roth, C.W., Louis, C., Kalush, F., Mural, R.J., Myers, E.W., Adams, M.D., Smith, H.O., Broder, S., Gardner, M.J., Fraser, C.M., Birney, E., Bork, P., Brey, P.T., Venter, J.C., Weissenbach, J., Kafatos, F.C., Collins, F.H. & Hoffman, S.L.
Science 2002 Oct 4;298(5591):129-49. Europe PMC

Immunity-related genes and gene families in Anopheles gambiae.
Christophides, G.K., Zdobnov, E., Barillas-Mury, C., Birney, E., Blandin, S., Blass, C., Brey, P.T., Collins, F.H., Danielli, A., Dimopoulos, G., Hetru, C., Hoa, N.T., Hoffmann, J.A., Kanzok, S.M., Letunic, I., Levashina, E.A., Loukeris, T.G., Lycett, G., Meister, S., Michel, K., Moita, L.F., Muller, H.M., Osta, M.A., Paskewitz, S.M., Reichhart, J.M., Rzhetsky, A., Troxler, L., Vernick, K.D., Vlachou, D., Volz, J., von Mering, C., Xu, J., Zheng, L., Bork, P. & Kafatos, F.C.
Science 2002 Oct 4;298(5591):159-65. Europe PMC

The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
Schell, M.A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M.C., Desiere, F., Bork, P., Delley, M., Pridmore, R.D. & Arigoni, F.
Proc Natl Acad Sci U S A 2002 Oct 29;99(22):14422-7. Europe PMC

Comparative analysis of protein interaction networks.
Bork, P.
Bioinformatics 2002 Oct;18 Suppl 2:S64. Europe PMC

Human non-synonymous SNPs: server and survey.
Ramensky, V., Bork, P. & Sunyaev, S.
Nucleic Acids Res 2002 Sep 1;30(17):3894-900. Europe PMC

InterPro: an integrated documentation resource for protein families, domains and functional sites.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R., Courcelle, E., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Griffith-Jones, S., Haft, D., Hermjakob, H., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Orchard, S., Pagni, M., Peyruc, D., Ponting, C.P., Servant, F. & Sigrist, C.J.
Brief Bioinform 2002 Sep;3(3):225-35. Europe PMC

NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
Andrade, M.A., Ciccarelli, F.D., Perez-Iratxeta, C. & Bork, P.
Genome Biol 2002 Aug 15;3(9):RESEARCH0047. Europe PMC

SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia.
Patel, H., Cross, H., Proukakis, C., Hershberger, R., Bork, P., Ciccarelli, F.D., Patton, M.A., McKusick, V.A. & Crosby, A.H.
Nat Genet 2002 Aug;31(4):347-8. Europe PMC

Predicting protein cellular localization using a domain projection method.
Mott, R., Schultz, J., Bork, P. & Ponting, C.P.
Genome Res 2002 Aug;12(8):1168-74. Europe PMC

The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations.
Bordo, D. & Bork, P.
EMBO Rep 2002 Aug;3(8):741-6. Europe PMC

Association of genes to genetically inherited diseases using data mining.
Perez-Iratxeta, C., Bork, P. & Andrade, M.A.
Nat Genet 2002 Jul;31(3):316-9. Europe PMC

A complex prediction: three-dimensional model of the yeast exosome.
Aloy, P., Ciccarelli, F.D., Leutwein, C., Gavin, A.C., Superti-Furga, G., Bork, P., Böttcher, B. & Russell, R.B.
EMBO Rep 2002 Jul;3(7):628-35. Europe PMC

Teamed up for transcription.
von Mering, C. & Bork, P.
Nature. 2002 Jun 20;417(6891):797-8. Europe PMC

Common exon duplication in animals and its role in alternative splicing.
Letunic, I., Copley, R.R. & Bork, P.
Hum Mol Genet. 2002 Jun 15;11(13):1561-7. Europe PMC

Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae.
Thomasova, D., Ton, L.Q., Copley, R.R., Zdobnov, E.M., Wang, X., Hong, Y.S., Sim, C., Bork, P., Kafatos, F.C. & Collins, F.H.
Proc Natl Acad Sci U S A 2002 Jun 11;99(12):8179-84. Europe PMC

Computing fuzzy associations for the analysis of biological literature.
Perez-Iratxeta, C., Keer, H.S., Bork, P. & Andrade, M.A.
Biotechniques 2002 Jun;32(6):1380-2, 1384-5. Europe PMC

Exploring MEDLINE abstracts with XplorMed.
Perez-Iratxeta, C., Bork, P. & Andrade, M.A.
Drugs Today (Barc) 2002 Jun;38(6):381-9. Europe PMC

Comparative assessment of large-scale data sets of protein-protein interactions.
von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. & Bork, P.
Nature 2002 May 23;417(6887):399-403. Europe PMC

The identification of functional modules from the genomic association of genes.
Snel, B., Bork, P. & Huynen, M.A.
Proc Natl Acad Sci U S A 2002 Apr 30;99(9):5890-5. Europe PMC

BSD: a novel domain in transcription factors and synapse-associated proteins.
Doerks, T., Huber, S., Buchner, E. & Bork, P.
Trends Biochem Sci 2002 Apr;27(4):168-70. Europe PMC

A versatile structural domain analysis server using profile weight matrices.
Schmidt, S., Bork, P. & Dandekar, T.
J Chem Inf Comput Sci 2002 Mar-Apr;42(2):405-7. Europe PMC

SHOT: a web server for the construction of genome phylogenies.
Korbel, J.O., Snel, B., Huynen, M.A. & Bork, P.
Trends Genet 2002 Mar;18(3):158-62. Europe PMC

AMOP, a protein module alternatively spliced in cancer cells.
Ciccarelli, F.D., Doerks, T. & Bork, P.
Trends Biochem Sci 2002 Mar;27(3):113-5. Europe PMC

Protein domain analysis in the era of complete genomes.
Copley, R.R., Doerks, T., Letunic, I. & Bork, P.
FEBS Lett 2002 Feb 20;513(1):129-34. Europe PMC

Genome and protein evolution in eukaryotes.
Copley, R.R., Letunic, I. & Bork, P.
Curr Opin Chem Biol 2002 Feb;6(1):39-45. Europe PMC

CASH – a beta-helix domain widespread among carbohydrate-binding proteins.
Ciccarelli, F.D., Copley, R.R., Doerks, T., Russell, R.B. & Bork, P.
Trends Biochem Sci 2002 Feb;27(2):59-62. Europe PMC

Functional organization of the yeast proteome by systematic analysis of protein complexes.
Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G. & Superti-Furga, G.
Nature 2002 Jan 10;415(6868):141-7. Europe PMC

Recent improvements to the SMART domain-based sequence annotation resource.
Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P. & Bork, P.
Nucleic Acids Res 2002 Jan 1;30(1):242-4. Europe PMC

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Fredman, D., Siegfried, M., Yuan, Y.P., Bork, P., Lehvaslaiho, H. & Brookes, A.J.
Nucleic Acids Res 2002 Jan 1;30(1):387-91. Europe PMC

Genomes in flux: the evolution of archaeal and proteobacterial gene content.
Snel, B., Bork, P. & Huynen, M.A.
Genome Res 2002 Jan;12(1):17-25. Europe PMC

Systematic identification of novel protein domain families associated with nuclear functions.
Doerks, T., Copley, R.R., Schultz, J., Ponting, C.P. & Bork, P.
Genome Res 2002 Jan;12(1):47-56. Europe PMC

Alternative splicing and genome complexity.
Brett, D., Pospisil, H., Valcarcel, J., Reich, J. & Bork, P.
Nat Genet 2002 Jan;30(1):29-30. Europe PMC

Proteinkomplexe und Netzwerke: Neue Herausforderungen für die Proteomik
Von Mering, C. and Bork, P.
Genomexpress 2/02, 2-4

Conservation of gene co-regulation in prokaryotes and eukaryotes.
Snel, B., Bork, P. & Huynen, M.A.
Trends Biotechnol. 2002 20(10) 410

Comparative genome analysis of the mollicutes.
Dandekar, T., Snel, B., Schmidt, S., Lathe, W., Suyama, M., Huynen, M. and Bork, P.
In "Mollicutes" (eds Herrmann et al.)

Sequence analysis of multidomain proteins: past perspectives and future directions.
Copley, R.R., Ponting, C.P., Schultz, J. & Bork, P.
Adv Protein Chem 2002;61:75-98. Europe PMC

The Spir actin organizers are involved in vesicle transport processes.
Kerkhoff, E., Simpson, J.C., Leberfinger, C.B., Otto, I.M., Doerks, T., Bork, P., Rapp, U.R., Raabe, T. & Pepperkok, R.
Curr Biol 2001 Dec 11;11(24):1963-8. Europe PMC

Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.
Ponting, C.P., Mott, R., Bork, P. & Copley, R.R.
Genome Res 2001 Dec;11(12):1996-2008. Europe PMC

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.
Huynen, M.A., Snel, B., Bork, P. & Gibson, T.J.
Hum Mol Genet 2001 Oct 1;10(21):2463-8. Europe PMC

XplorMed: a tool for exploring MEDLINE abstracts.
Perez-Iratxeta, C., Bork, P. & Andrade, M.A.
Trends Biochem Sci 2001 Sep;26(9):573-5. Europe PMC

Evolution of tuf genes: ancient duplication, differential loss and gene conversion.
Lathe WC, 3rd & Bork, P.
FEBS Lett 2001 Aug 3;502(3):113-6. Europe PMC

Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells.
Woerner, S.M., Gebert, J., Yuan, Y.P., Sutter, C., Ridder, R., Bork, P. & von Knebel Doeberitz, M.
Int J Cancer 2001 Jul 1;93(1):12-9. Europe PMC

Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens.
Linnebacher, M., Gebert, J., Rudy, W., Woerner, S., Yuan, Y.P., Bork, P. & von Knebel Doeberitz, M.
Int J Cancer 2001 Jul 1;93(1):6-11. Europe PMC

Inversions and the dynamics of eukaryotic gene order.
Huynen, M.A., Snel, B. & Bork, P.
Trends Genet 2001 Jun;17(6):304-6. Europe PMC

Comparison of ARM and HEAT protein repeats.
Andrade, M.A., Petosa, C., O'Donoghue, S.I., Muller, C.W. & Bork, P.
J Mol Biol 2001 May 25;309(1):1-18. Europe PMC

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
Shevchenko, A., Sunyaev, S., Loboda, A., Bork, P., Ens, W. & Standing, K.G.
Anal Chem 2001 May 1;73(9):1917-26. Europe PMC

Prediction of deleterious human alleles.
Sunyaev, S., Ramensky, V., Koch, I., Lathe W, 3rd, Kondrashov, A.S. & Bork, P.
Hum Mol Genet 2001 Mar 15;10(6):591-7. Europe PMC

DDT -- a novel domain in different transcription and chromosome remodeling factors.
Doerks, T., Copley, R. & Bork, P.
Trends Biochem Sci 2001 Mar;26(3):145-6. Europe PMC

The draft sequences. Filling in the gaps.
Bork, P. & Copley, R.
Nature 2001 Feb 15;409(6822):818-20. Europe PMC

Genome speak.
Bork, P. & Copley, R.
Nature 2001 Feb 15;409(6822):815. Europe PMC

Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35].
Schultz, J., Jones, T., Bork, P., Sheer, D., Blencke, S., Steyrer, S., Wellbrock, U., Bevec, D., Ullrich, A. & Wallasch, C.
Genomics 2001 Feb 1;71(3):368-70. Europe PMC

Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms.
Sunyaev, S., Lathe W, 3rd & Bork, P.
Curr Opin Struct Biol 2001 Feb;11(1):125-30. Europe PMC

The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival.
Becker, S., Gehrsitz, A., Bork, P., Buchner, S. & Buchner, E.
Gene 2001 Jan 10;262(1-2):15-22. Europe PMC

Evolution of prokaryotic gene order: genome rearrangements in closely related species.
Suyama, M. & Bork, P.
Trends Genet 2001 Jan 1;17(1):10-13. Europe PMC

Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes.
Eisenhaber, B., Bork, P. & Eisenhaber, F.
Protein Eng 2001 Jan;14(1):17-25. Europe PMC

Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Iyer, L.M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A.R., Zhulin, I.B. & Koonin, E.V.
Genome Biol 2001;2(12):RESEARCH0051. Europe PMC

TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture.
Herold, A., Suyama, M., Rodrigues, J.P., Braun, I.C., Kutay, U., Carmo-Fonseca, M., Bork, P. & Izaurralde, E.
Mol Cell Biol 2000 Dec;20(23):8996-9008 Europe PMC

Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways.
Copley, R.R. & Bork, P.
J Mol Biol 2000 Nov 3;303(4):627-41. Europe PMC

Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.
Gonczy, P., Echeverri, G., Oegema, K., Coulson, A., Jones, S.J., Copley, R.R., Duperon, J., Oegema, J., Brehm, M., Cassin, E., Hannak, E., Kirkham, M., Pichler, S., Flohrs, K., Goessen, A., Leidel, S., Alleaume, A.M., Martin, C., Ozlu, N., Bork, P. & Hyman, A.A.
Nature 2000 Nov 16;408(6810):331-6. Europe PMC

Gene context conservation of a higher order than operons.
Lathe, W.C., Snel, B. & Bork, P.
Trends Biochem Sci 2000 Oct;25(10):474-9. Europe PMC

GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
Doerks, T., Strauss, M., Brendel, M. & Bork, P.
Trends Biochem Sci 2000 Oct;25(10):483-5. Europe PMC

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Snel, B., Lehmann, G., Bork, P. & Huynen, M.A.
Nucleic Acids Res 2000 Sep 15;28(18):3442-4. Europe PMC

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Dandekar, T., Huynen, M., Regula, J.T., Ueberle, B., Zimmermann, C.U., Andrade, M.A., Doerks, T., Sanchez-Pulido, L., Snel, B., Suyama, M., Yuan, Y.P., Herrmann, R. & Bork, P.
Nucleic Acids Res 2000 Sep 1;28(17):3278-88. Europe PMC

EST analysis online: WWW tools for detection of SNPs and alternative splice forms.
Brett, D., Lehmann, G., Hanke, J., Gross, S., Reich, J. & Bork, P.
Trends Genet 2000 Sep;16(9):416-8. Europe PMC

SNP frequencies in human genes an excess of rare alleles and differing modes of selection.
Sunyaev, S.R., Lathe WC, 3rd, Ramensky, V.E. & Bork, P.
Trends Genet. 2000 Aug;16(8):335-7. Europe PMC

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences.
Huynen, M., Snel, B., Lathe, W. & Bork, P.
Genome Res 2000 Aug;10(8):1204-10. Europe PMC

Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins.
Suyama, M., Doerks, T., Braun, I.C., Sattler, M., Izaurralde, E. & Bork, P.
EMBO Rep. 2000 Jul;1(1):53-8. Europe PMC

NAIL-Network Analysis Interface for Linking HMMER results.
Sanchez-Pulido, L., Yuan, Y.P., Andrade, M.A. & Bork, P.
Bioinformatics 2000 Jul;16(7):656-7. Europe PMC

Automated annotation of GPI anchor sites: case study C. elegans.
Eisenhaber, B., Bork, P., Yuan, Y., Loffler, G. & Eisenhaber, F.
Trends Biochem Sci 2000 Jul;25(7):340-1. Europe PMC

L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7.
Doerks, T., Bork, P., Kamberov, E., Makarova, O., Muecke, S. & Margolis, B.
Trends Biochem Sci 2000 Jul;25(7):317-8. Europe PMC

Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines.
Dimopoulos, G., Casavant, T.L., Chang, S., Scheetz, T., Roberts, C., Donohue, M., Schultz, J., Benes, V., Bork, P., Ansorge, W., Soares, M.B. & Kafatos, F.C.
Proc Natl Acad Sci U S A 2000 Jun 6;97(12):6619-24 Europe PMC

Automated extraction of information in molecular biology.
Andrade, M.A. & Bork, P.
FEBS Lett 2000 Jun 30;476(1-2):12-7. Europe PMC

More than 1,000 putative new human signalling proteins revealed by EST data mining.
Schultz, J., Doerks, T., Ponting, C.P., Copley, R.R. & Bork, P.
Nat Genet 2000 Jun;25(2):201-4 Europe PMC

Exploitation of gene context.
Huynen, M., Snel, B., Lathe, W. & Bork, P.
Curr Opin Struct Biol 2000 Jun;10(3):366-70. Europe PMC

EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.
Brett, D., Hanke, J., Lehmann, G., Haase, S., Delbruck, S., Krueger, S., Reich, J. & Bork, P.
FEBS Lett. 2000 May 26;474(1):83-6. Europe PMC

Homology-based method for identification of protein repeats using statistical significance estimates.
Andrade, M.A., Ponting, C.P., Gibson, T.J. & Bork, P.
J Mol Biol 2000 May 5;298(3):521-37 Europe PMC

Towards a structural basis of human non-synonymous single nucleotide polymorphisms.
Sunyaev, S., Ramensky, V. & Bork, P.
Trends Genet 2000 May;16(5):198-200. Europe PMC

REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export.
Stutz, F., Bachi, A., Doerks, T., Braun, I.C., Seraphin, B., Wilm, M., Bork, P. & Izaurralde, E.
RNA 2000 Apr;6(4):638-50. Europe PMC

Powers and pitfalls in sequence analysis: the 70% hurdle.
Bork, P.
Genome Res 2000 Apr;10(4):398-400. Europe PMC

The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization.
Otto, I.M., Raabe, T., Rennefahrt, U.E., Bork, P., Rapp, U.R. & Kerkhoff, E.
Curr Biol 2000 Mar 23;10(6):345-8. Europe PMC

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem.
Isaksson, A., Landegren, U., Syvanen, A.C., Bork, P., Stein, C., Ortigao, F. & Brookes, A.J.
Eur J Hum Genet 2000 Feb;8(2):154-6. Europe PMC

SMART: a web-based tool for the study of genetically mobile domains.
Schultz, J., Copley, R.R., Doerks, T., Ponting, C.P. & Bork, P.
Nucleic Acids Res 2000 Jan 1;28(1):231-4. Europe PMC

HGBASE: a database of SNPs and other variations in and around human genes.
Brookes, A.J., Lehvaslaiho, H., Siegfried, M., Boehm, J.G., Yuan, Y.P., Sarkar, C.M., Bork, P. & Ortigao, F.
Nucleic Acids Res 2000 Jan 1;28(1):356-60 Europe PMC

Genome evolution. Gene fusion versus gene fission.
Snel, B., Bork, P. & Huynen, M.
Trends Genet 2000 Jan;16(1):9-11. Europe PMC

Individual variation in protein-coding sequences of human genome.
Sunyaev, S., Hanke, J., Brett, D., Aydin, A., Zastrow, I., Lathe, W., Bork, P. & Reich, J.
Adv Protein Chem 2000;54:409-37. Europe PMC

Evolution of domain families.
Ponting, C.P., Schultz, J., Copley, R.R., Andrade, M.A. & Bork, P.
Adv Protein Chem 2000;54:185-244. Europe PMC

Exploitation of gene context to infer evolution and to predict function.
Bork, P., Snel, B., Lehmann, G., Suyama, M., Dandekar, T., Lathe, W. & Huynen, M.
In "Comparative Genomics", Sankoff, D. & Nadeau, J.H. (eds.) Kluwer Acad. Publ. pp. 281-294

Analysis of amino acid sequence.
Bork, P. (ed.), Acad. Press
Advances in Protein Chemistry

Genome and proteome informatics
Bork, P. & Eisenberg, D.
Curr. Opin. Struct. Biol. 2000 10 341-342

Preface: Protein sequence analysis
Bork, P.
Adv. Prot. Chem. 2000 54 xi-xv

The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins.
Liu, Z., Macias, M.J., Bottomley, M.J., Stier, G., Linge, J.P., Nilges, M., Bork, P. & Sattler, M.
Structure Fold Des 1999 Dec 15;7(12):1557-66 Europe PMC

A point of entry into genomics.
Bork, P. & Huynen, M.A.
Nat Genet. 1999 Nov;23(3):273. Europe PMC

Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes.
Sunyaev, S., Hanke, J., Aydin, A., Wirkner, U., Zastrow, I., Reich, J. & Bork, P.
J Mol Med 1999 Nov;77(11):754-60 Europe PMC

Phospholipases A2 and Wnts are unlikely to share a common ancestor.
Copley, R.R., Ponting, C.P. & Bork, P.
Curr Biol. 1999 Oct 7;9(19):R718-9. Europe PMC

A lipid-binding domain in Wnt: a case of mistaken identity?
Barnes, M.R., Russell, R.B., Copley, R.R., Ponting, C.P., Bork, P., Cumberledge, S., Reichsman, F. & Moore, H.M.
Curr Biol 1999 Oct 7;9(19):R717-9 Europe PMC

Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Dandekar, T., Schuster, S., Snel, B., Huynen, M. & Bork, P.
Biochem J 1999 Oct 1;343 Pt 1:115-24 Europe PMC

Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.
Smalla, M., Schmieder, P., Kelly, M., Ter Laak, A., Krause, G., Ball, L., Wahl, M., Bork, P. & Oschkinat, H.
Protein Sci 1999 Oct;8(10):1954-61 Europe PMC

Alternative splicing of human genes: more the rule than the exception?
Hanke, J., Brett, D., Zastrow, I., Aydin, A., Delbruck, S., Lehmann, G., Luft, F., Reich, J. & Bork, P.
Trends Genet 1999 Oct;15(10):389-90 Europe PMC

Prediction of potential GPI-modification sites in proprotein sequences.
Eisenhaber, B., Bork, P. & Eisenhaber, F.
J Mol Biol 1999 Sep 24;292(3):741-58 Europe PMC

Associative database of protein sequences.
Hanke, J., Lehmann, G., Bork, P. & Reich, J.G.
Bioinformatics 1999 Sep;15(9):741-8 Europe PMC

Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures.
Muller, S.A., Sasaki, T., Bork, P., Wolpensinger, B., Schulthess, T., Timpl, R., Engel, A. & Engel, J.
J Mol Biol 1999 Aug 27;291(4):801-13 Europe PMC

A latrophilin/CL-1-like GPS domain in polycystin-1
Ponting, C.P., Hofmann, K. & Bork, P.
Curr Biol 1999 Aug 26;9(16):R585-8 Europe PMC

Variation and evolution of the citric-acid cycle: a genomic perspective.
Huynen, M.A., Dandekar, T. & Bork, P.
This is a review article.
Trends Microbiol 1999 Jul;7(7):281-91 Europe PMC

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Eisenhaber, F. & Bork, P.
Bioinformatics 1999 Jul-Aug;15(7-8):528-35 Europe PMC

Domains in plexins: links to integrins and transcription factors.
Bork, P., Doerks, T., Springer, T.A. & Snel, B.
Trends Biochem Sci 1999 Jul;24(7):261-3 Europe PMC

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.
Ponting, C.P., Aravind, L., Schultz, J., Bork, P. & Koonin, E.V.
J Mol Biol 1999 Jun 18;289(4):729-45 Europe PMC

A novel transactivation domain in parkin
Morett, E. & Bork, P.
Trends Biochem Sci 1999 Jun;24(6):229-31 Europe PMC

Protein families in multicellular organisms.
Copley, R.R., Schultz, J., Ponting, C.P. & Bork, P.
This is a review article.
Curr Opin Struct Biol 1999 Jun;9(3):408-15 Europe PMC

No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho
Ponting, C.P., Bork, P., Schultz, J. & Aravind, L.
Trends Biochem Sci 1999 May;24(5):177-8 Europe PMC

SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Ponting, C.P., Schultz, J., Milpetz, F. & Bork, P.
Nucleic Acids Res 1999 Jan 1;27(1):229-32 Europe PMC

Genome phylogeny based on gene content.
Snel, B., Bork, P. & Huynen, M.A.
Nat Genet 1999 Jan;21(1):108-10 Europe PMC

Lateral Gene transfer, genome surveys and the phylogeny of prokaryotes.
Huynen, M.A., Snel, B. & Bork, P.
Science 1999 286(5444) 1443a

Sequence analysis, dotplot, aligning sequences, indels and gap-penalty
Gibson, T. & Bork, P.
In "Encyclopedia of Molecular Biology", T. Creighton (ed.), Wiley & Sons Inc. New York. 86-90; 765-766; 961-962; 1252; 2220-2324

Genome comparisons to monitor molecular evolution.
Bork, P., Dandekar, T., Snel, B. & Huynen, M.A.
In "Microbiology and Infection", Goebel, U.B., Ruf. B.R.(ed.), Einhorn-presse Verlag, Reinbek, 80-92

Bioinformatik (editorial)
Bork, P.
Biospektrum 1999 3 172

Applying logic programming ro derive novel functional information of genomes.
Bansal, A.K., & Bork, P.
In "Lecture notes in computer science 1551: Practical aspects of declarative languages", Gupta, G. (ed.), Springer Verlag, 275-289

Homology-based gene prediction using neural nets.
Cai, Y. & Bork, P.
Anal Biochem 1998 Dec 15;265(2):269-74. Europe PMC

Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues.
Willeke, F., Ridder, R., Bork, P., Klaes, R., Mechtersheimer, G., Schwarzbach, M., Zimmer, D., Kloor, M., Lehnert, T., Herfarth, C. & von Knebel Doeberitz, M.
Mol Carcinog 1998 Dec 23(4) 195-200 Europe PMC

Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase.
Eisenhaber, B., Bork, P. & Eisenhaber, F.
Protein Eng 1998 Dec 11(12) 1155-1161 Europe PMC

Predicting function: from genes to genomes and back.
Bork, P., Dandekar, T., Diaz-Lazcoz, Y., Eisenhaber, F., Huynen, M. & Yuan, Y.
This is a review article.
J Mol Biol 1998 Nov 6 283(4) 707-725 Europe PMC

Conservation of gene order: a fingerprint of proteins that physically interact.
Dandekar, T., Snel, B., Huynen, M. & Bork, P.
Trends Biochem Sci 1998 Sep;23(9):324-8. Europe PMC

Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC.
Morett, E. & Bork, P.
FEBS Lett 1998 Aug 14 433(1-2) 108-112 Europe PMC

Homology-based fold predictions for Mycoplasma genitalium proteins.
Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S., Yuan, Y. & Bork, P.
J Mol Biol 1998 Jul 17;280(3):323-6. Europe PMC

Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries.
Kharrat, A., Millevoi, S., Baraldi, E., Ponting, C.P., Bork, P. & Pastore, A.
Biochim Biophys Acta 1998 Jun 11;1385(1):157-64. Europe PMC

Protein annotation: detective work for function prediction.
Doerks, T., Bairoch, A. & Bork, P.
This is a review article.
Trends Genet 1998 Jun 14(6) 248-250 Europe PMC

SMART, a simple modular architecture research tool: identification of signaling domains.
Schultz, J., Milpetz, F., Bork, P. & Ponting, C.P.
Proc Natl Acad Sci U S A 1998 May 26 95(11) 5857-5864 Europe PMC

Measuring genome evolution.
Huynen, M.A. & Bork, P.
This is a review article.
Proc Natl Acad Sci U S A 1998 May 26 95(11) 5849-5856 Europe PMC

Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis.
Schwirzke, M., Gnirke, A., Bork, P., Tarin, D. & Weidle, U.H.
Anticancer Res 1998 May-Jun;18(3A):1409-21. Europe PMC

Differential genome analysis applied to the species-specific features of Helicobacter pylori.
Huynen, M., Dandekar, T. & Bork, P.
FEBS Lett 1998 Apr 10;426(1):1-5. Europe PMC

Wanted: subcellular localization of proteins based on sequence.
Eisenhaber, F. & Bork, P.
Trends Cell Biol 1998 Apr;8(4):169-70. Europe PMC

Predicting functions from protein sequences--where are the bottlenecks?
Bork, P. & Koonin, E.V.
This is a review article.
Nat Genet 1998 Apr 18(4) 313-318 Europe PMC

Merging extracellular domains: fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins
Beckmann, G., Hanke, J., Bork, P. & Reich, J.G.
J Mol Biol 1998/02/06 275(5) 725-730 Europe PMC

Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases.
Bork, P., Dandekar, T., Eisenhaber, F. & Huynen, M.
J Mol Med 1998 Feb;76(2):77-9. Europe PMC

Towards detection of orthologues in sequence databases.
Yuan, Y.P., Eulenstein, O., Vingron, M. & Bork, P.
Bioinformatics 1998;14(3):285-9 Europe PMC

Elementary modes analysis illustrated with human red cell metabolism.
Schuster, S., Fell, D.A., Pfeiffer, T., Dandekar, T. & Bork, P.
In "BioThermoKinectis in the Post Genomic Era," Larsson, C., Pahlman, I.-L. & Gustafsson, L. (eds.), 1998, Chalmers, Goeteborg, pp. 332-339

Sequence and structure of proteins
Eisenhaber, F. & Bork, P.
In "Recombinant protein, monoclonal antibodies and therapeutic genes," (series Biotechnology, 2nd. Edition), 1998, Rehm, H.-J. & Reed, G. (eds.), Wiley-VCH, Weinheim

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Dandekar, T., Beyer, K., Bork, P., Kenealy, M.R., Pantopoulos, K., Hentze, M., Sonntag-Buck, V., Flouriot, G., Gannon, F. & Schreiber, S.
Bioinformatics 1998;14(3):271-8 Europe PMC

Frame: detection of genomic sequencing errors.
Brown, N.P., Sander, C. & Bork, P.
Bioinformatics 1998 14(4) 367-371 Europe PMC

Deriving biological knowledge from genomic sequence.
Bork, P. & Eisenberg, D.
Curr Opin Struc Biol 1998 8 331-332

Automated pair-wise comparisons of microbial genomes.
Bansal, A.K., Bork, P. & Stuckey
Mathematical Modelling and Scientific Computing 1998 9 1-23

Secreted fringe-like signaling molecules may be glycosyltransferases
Yuan, Y.P., Schultz, J., Mlodzik, M. & Bork, P.
Cell 1997 Jan 10;88(1):9-11 Europe PMC

Pleckstrin's repeat performance: a novel domain in G-protein signaling?
Ponting, C.P. & Bork, P.
Trends Biochem Sci 1996 Jul;21(7):245-6 Europe PMC

Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search.
Bork, P., Gellerich, J., Groth, H., Hooft, R. & Martin, F.
Protein Sci 1995 Feb;4(2):268-74. Europe PMC